Possible Distributor Problems???

[kytarheel71]

1987 Prelude Si Auto FI
need some help here guys. First off a little backround. Just had my ludes engine rebuilt. Wasnt anything really wrong with it in the first place just leaked oil, coolant etc everywhere. My son rebuilt it at his votech class at school. Now it never really ran good in the first place but it did run...rough. i always had the idle problems as usual, trouble starting after warm,(with sometimes a kickback on startup). It just never ran right, get my meaning.
Now i have replaced just about everything u can replace on her except for the distributor. The problem is i have a rough idle no matter what we have tried and it seems like a miss in it too or maybe its just the same thing. we have tried a different iacv, played with idle sdjust screw, new vacuum lines etc. We cant seem to get it in time or so we think. we have checked with timing light but cant get it to line up correctly, the red mark with the pointer. my question is we have found different instructions on how to check and adjust the ign. timing. Does anyone know the definite right way and can my distributor be partly shot or something. it does have a new dist cap also. also they did the TDC getup correctly at the shop too just in case that was a thought.
Really need some help because we are so close to getting her running good after almost 3 yrs of headaches.
I followed the shop manual but no matter how much we rotate the distributor the marks still wont line up correctly. The cam timing is correct also.We looked up on the internet and found several different sets of instructions that conflict with each other. we also unhooked the vacuum advance lines and plugged them while doing this in case that is a question.

[spiffyguido]

Before checking the timing with a timing light, have you verified that the cam gear is lined up correctly on the belt?