The runners actually dont intrude into the plenum area at all. They end right where they meet the plenum.
I agree that the cam must be a major weak link, because honestly if you look at the top end you have to wonder why it isnt rated much higher than the 3.0. It seems likely to me that a stock 3.3 longblock could make 170-180 hp with thorough tuning, even without changing any parts.
I have been running cams through Desktop Dyno and there is nearly a 30-40 HP gain with the right cam, which puts it slightly over the 2001 and up version of this engine. Most of the gain is from 4000 RPM up on the different cams I have input with no loss of low end. BTW, Desktop Dyno was nearly dead-on to factory rated power when I put all the '94-95 specs in.
I also think intake is a part of it too. The engineers optimized low end torque at the expense of horsepower. It needs a little shorter or larger runner to gain some top end. The Intrepid intake would be a good thing to try if you can cut the elbow off it.
That being said, now I have a Megasquirted 3.3, I think the factory was also conservative on the tuning to save the A604 transmission. My engine screams with a 60mm throttle body, 3" exhaust, and a little tuning. I am using the 160 HP '95 van engine but it seems
nearly as strong as my 225 horse 2.0 turbo was. The engine falls over at about 5000 RPM, so that does back up the cam theory, and verifies the published HP/TQ graphs I have seen.