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This is constructive criticism, part of the learning process, You made the flow chart seem much harder than it actually is, I understand that experience plays a big part, do not let it intimidate you, it should not have taken any longer than 15-30 minutes to get to the actual circuit creating the problem.
1)Check for fault codes - YES (Code 54 needs to be diagnosed 1st, as long as it is a real code that was not set accidently during diagnostics)

If you have a Code 54 stored in memory you have a HEP circuit issue.
Code 54 is "Loss Of Fuel Sync Signal".
The fuel sync signal tells the controller where #1 cylinder is located on the Turbo cars so it can pulse the injectors in the proper sequence.
If the controller loses either the Crank/RPM signal or the Fuel Sync Signal it will not actuate the ASD Relay, the ASD Relay provides power to the fuel pump, + coil and injectors.
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Clear the codes, be sure they cleared, crank the engine 7-10 seconds and recheck codes.
Did Code 54 return?


You also need to check/charge your battery, 9.3 volts at the + coil is not acceptable, you need 12 volts present, 12.60 volts = a fully charged battery. (2.1 volts per cell).

If it turns out to be the HEP...
1)Do Not Bend the HEP Wiring as the factory had it or you will damage the internal wiring.
2)A new replacement does not always = a good/functioning replacement.

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If after replacing the HEP or determining the Code was not real then you need to continue with the flow chart.
1)Fault Codes - YES/NO If YES, what are the codes? (Code 23 is not relevant)
If NO, continue.
2)Spark - YES/NO, If NO, continue
3)Remove the distributor cap and crank the engine, is the distributor turning? YES/NO
If NO, check the timing belt, intermediate shaft and distributor.
If YES, continue.
4)Manually actuate the ASD Relay, is power present at the + coil, fuel pump and injectors? YES/NO.
If NO, diagnose the ASD Relay circuit.
If YES remove the jumper wire from the diagnostic connector and continue.
5)Connect a test lamp to the + coil and a known good ground, crank the engine and check for power (battery voltage) at the + coil, is power (12 volts) present? YES/NO
If NO, diagnose the HEP circuit.
If YES, continue.
6)Move your test lamp from the + coil to the - coil terminal and crank the engine, the test lamp should flash on/off constantly as the engine is cranked.
Did the test lamp illuminate and flash on/off? YES/NO
If NO, diagnose the coil control circuit
If YES, test the coil itself.

One other thing since you said the engine was just rebuilt, be sure all controller/body grounds are securely connected.
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1)9.6 volts is normal battery voltage when cranking the engine, lower than 9.00 volts cranking = a faulty battery or a starter with excessive draw.
2)If you have battery voltage at the + coil when cranking you Do Not have a HEP issue.
As long as the engine controller is seeing a crank/rpm and fuel sync signal (turbo only) it will actuate the ASD Relay which will provide power to the + coil, fuel pump and injectors, No Signal(s) = No ASD Actuation = No Power to + Coil.
I have seen Code 54 set in memory without a HEP issue, sometimes on a car that runs, why?
My assumption is the controller is not seeing the proper signal for some other reason (stray voltage from another faulty circuit?) so it sets the code.
3)Not quite sure what your results in step 6 were...Did the test lamp flash on/off while cranking.
You said the test lamp became very dim after cranking, did battery voltage also drop, has this battery been tested?

4)Test the coil itself before going further.
a)Verify coil primary and secondary resistance is correct.
1.34 - 1.55 ohms on the primary
9000 - 11,700 ohms secondary
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b)Be sure the battery is fully charged. (12.60 volts)
c)Disconnect the - coil lead from the coil
d)Remove the coil secondary wire from the distributor cap and place it 1/4" from a known good ground.
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e)Connect a jumper wire to the coil terminal
f)Manually actuate the ASD Relay and verify battery voltage is present at the + coil.
g)With all of the above steps in place take the free end of your jumper wire and momentarily touch to ground and remove.
Each time you touch and remove the jumper from ground you should have a good strong spark from the coil secondary wire to ground.
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Again, just to verify, there is constant battery voltage at the + coil when cranking?
If there is you do not have a HEP issue.
If you have battery voltage at the + coil with the ASD relay manually actuated and you touch/remove the jumper from a known good ground and there is no spark from the coil secondary wire to ground then the coil is faulty or the coil secondary wire is open or has excessive resistance.
 

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I am going to send you the "No Start/No Spark" diagnostics straight from the Chrysler Powertrain Diagnostics Manual.
The only difference is this is for 1990 2.2L/2.5L Turbo engines, if asked to check/trace wiring to the controller you need to use your 88 wiring instead of the 90 images shown in the diagnostics.
I will not have time to do it today but will get it to you by the end of the weekend.
 

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1)Is there a factory or aftermarket alarm system in this vehicle?
2)Is TPS closed throttle voltage below 2.50 volts?
3)Do all controller grounds have less than 5 ohms resistance to ground?

Here are the No Start/No Spark diagnostics from the Chrysler Powertrain Diagnostics Manual, remember, this is from a 1990 FSM with a SBEC, you will need to use the pinout for an 88 SMEC when you run these diagnostics.
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Multiple posts have been made since you sent me the results from your diagnostics in Post #29, I am ignoring/not reading any of those posts or listening to any other ideas until these two things are corrected/repaired.
1)Battery Voltage
NAJ, Aug 4:
Again, just to verify, there is constant battery voltage at the + coil when cranking?
If there is you do not have a HEP issue.
Not full battery voltage, no. 9.3 to 9.5V
I think we have ruled out the HEP.

a)What is battery voltage at the + coil with the ASD Relay manually actuated with the KOEO? (Key On, Engine Off)
If it is above 12 volts then proceed to step 2, if it is not, continue with step 1.
The engine controller needs a minimum of 10 volts to function properly, 9.3-9.6 volts is NOT acceptable.
The battery needs to be fully charged and tested under load to be sure it is good, static battery voltage has to be in the 12.4-12.6 range and no lower than 9.6 volts cranking (starter draw).
If the battery voltage is within the correct range of 12.50 volts across the battery terminals (and battery posts, check both ways to be sure there is not excessive resistance between the battery terminals and battery posts.) but you only have 9.5 volts at the + coil with the ASD manually actuated then you have excessive resistance in the ASD output circuit or a short in the ASD output circuit to another circuit that is drawing away voltage.
Until you get proper battery voltage at the battery itself and then proper voltage at the + coil with the ASD manually actuated you CANNOT proceed any further.

2)Ignition Coil

NAJ, Aug 4:
If you have battery voltage at the + coil with the ASD relay manually actuated and you touch/remove the jumper from a known good ground and there is no spark from the coil secondary wire to ground then the coil is faulty or the coil secondary wire is open or has excessive resistance.
No spark. I have tried two coils and the secondary coil wire seems to be fine with about 502 ohms per in of resistance.
a)If you have proper voltage (Minimum 12 volts) at the + coil with the ASD Relay manually actuated and you make and break the connection to the - coil and there is no spark from the secondary coil wire to ground then that coil is faulty or you did something wrong.
If you cannot get 12 volts to the + coil with the ASD manually actuated you can remove both wires from the coil, connect another 12 volt power source to the + coil and make/break the - coil connection to see if it makes a difference.
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Until these two things are corrected you cannot proceed further.
 

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Still would like to know if code 54 is still present, and if so why???? Has anyone ever seen one of these car run with that code on? Not likely.
A few times members of this group have had a car that was running (with other driveabilty issues) and set a Code 54, to this day I still do not know why or how, the only explanation I have is that stray voltage (from somewhere) is interfering with the and/or changing the sync signal the controller is seeing, sort of like an intermittent "hiccup". Remember, the controller only see's the sync signal one time per distributor revolution.
 

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"There is a spark from the - post of the coil to ground."

You will get a small spark at the coil - terminal each time you make/break the connection, what you are looking for is spark from the coil secondary wire to ground each time you break the connection at the - coil terminal.
I find it easier to use a jumper wire and make/break the connection at the - battery terminal rather than at the - coil terminal itself.


I do not like that you are losing 1.4 volts from the kill switch to the coil + terminal.
Without manually actuating the ASD Relay, with the key on/engine off what is voltage reading at the ASD Relay connector Red and Dark Blue wires?
 

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We are on page 3 with this issue, lets get back to the beginning/basics, before we get in so deep "we cannot see the forest for the trees".
This page and the questions asked will get us up to speed on where we stand so we can proceed further knowing the basics have been checked and verified and we do not have to scroll through 3 pages to find the answers.
1)You have a cranks but will not start condition and have no spark?
Yes/No

2)
You have a Code 54 set in memory?
Yes/No If Yes, continue
a)
After clearing the codes, verifying the codes did clear and cranking the engine for 7-10 seconds did the Code 54 return?
Yes/No If Yes, continue
b)
You ran the diagnostics for Code 54 (in post 25) and the end conclusion was?
c)You tried a "known good" HEP and the result was?
d)You verified the shutter wheel in the distributor was secure.
Yes/No
e)
You verified that you have the correct distributor for a turbo car?
Yes/No
f)
Are there any aftermarket accessories underhood that could be causing electrical interference/electrical noise or that could possibly be inducing a small voltage into another circuit? (Higher voltage harness's not properly shielded or running parallel to each other, Sound Systems, Security Alarm, Remote Start, etc.)
Yes/No

3)
You ran the No Start diagnostics from the FSM (in post 25) and the end conclusion was?

4)You also checked closed throttle TPS voltage but you were not exactly sure about how to check.
(closed throttle voltage above 2.50 volts = clear flood mode which = no fuel)
a)With the KOEO use your digital voltmeter to backprobe the VT/WT wire of the TPS connector, does the meter read 5 volts (4.90 is OK).
Yes/No If Yes, continue
b)
Using your digital voltmeter backprobe the OR/DB and BK/LB wires, voltage should read between .30 and .90 volts?
c)Is TPS closed throttle voltage within specs?
Yes/No
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5)
You verified all power feeds into and out of the controller all have the correct voltage?
a)SMEC 14 Pin Connector
Cavity 1 - 8 volt output
Cavity 3 - 12 volt output
Cavity 4 - 12 volt input
b)SMEC 60 Pin Connector
Cavity 12 - 12 volt input
Cavity 13 - 5 volt output
Cavity 52 - 8 volt input
c)Do all controller power feeds have the correct voltage?
Yes/No

6)
You verified all controller ground circuits have < 5 ohms resistance to ground?
a)SMEC 14 Pin Connector
Cavities 2, 6, 7
b)SMEC 60 Pin Connector
Cavities 4, 5, 15, 16
c)Do all controller ground circuits have < 5 ohms resistance to ground?
Yes/No
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