I know this is an old thread - Jaydos not sure if your problems are resolved yet.
im in a similar boat, trying to get a 16v big port running after a long time off the road and I have the exact symptoms described. Usually a inlet or exhaust misfire on cold start, rough idle, give it a bit of gas, try a few times and eventually it runs smooth... once its warm seems to start fine. it's almost like a "frog in the throat", once cleared it feels good and idles well.
So far I have replaced a fuel pump, coil, cap, rotor, leads and plugs. Have reset timing to factory. it usually starts OK when the TPS is disconnected.
Unfortunately I dont have a working engine check light, there is a bit of damage on my ecu board where the W wire goes and i havent been able to get it to work. So i am in the dark just replacing bits one at a time. trying to get my hands on another ecu, TPS and MAP sensor.
I know that doesnt help u at allbut i've just been searching the forum and this thread describes my engines symptoms exactly.. i'll let u know how i go
OK it turns out I have a sticky lifter on the #4 inlet side valve that is staying open and after a bit of warming up it must loosen up. As far as i can tell all the fuel, ignition and sensors are OK. That explains the misfires. As I said the engine had sat a while and there is years of crusty oil build up in the valve train.
I will try and remove it, hopefully i can get it out, and clean or replace the bucket.