Read the all links I gave you. Those should be very helpful. They guided me to do my conversion just fine. I did it in three steps.
Build up the engine and transmission outside the car.
Wire the car while the engine and transmission it out.
Install hoses and intercooler after engine/transmission are in and wiring and computer are done.
In your case, I'd test the compression and make sure the bottom end is good. If it is, pull the head and install everything you need, set it aside. Do the wiring and computer, then, reinstall the head, and do the intercooler piping last.
As GLHNSLHT2 said,
do not use the TI intake manifold's bolt on TII intake manifold, the TI bolts are just short enough to be thread on, but they
will strip the threads out of the head as you tighten them. Don't ask me how I know. :bang head
Worthy the project at the end.