nfccws

yes i realize this is a double post but my original in the specific tech section got 70 hits n no responses,so imma make another one here in the more open area.

ok im the new guy here but im hoping this site is better than hondatech for help with what was a minor issue but became a big issue tonight..
i have a 97 EK coupe with a b18a1 swap,it has a b18b1 manifold to work with the stock motor harness on the car(modded to work on an LS) far as the map or maf sensor goes
Now since i got the car from a buddy n we swapped my A1 in place of his F*cked turbo LS B1(that ran fine when he had it not boosted) ive had a small hesitation when driving,like im going along in 4th at 45mph or so and i let off the gas to slow for the inevitable slow *** driver on rt30 and it would cut out a small bit like a hesitation..
I replaced the dizzy,injectors(had 310cc to n went to 240cc) and it improved a bit and ran better,now in the last few days the alternator died and i got a replacement today and that solved my charging/dead battery issue but after i got it running it was fine at 1st but tonight it hesitated and was missing like crazy! i could shift fine and the rpms didnt jump but it was far from smooth what so ever,it sounded like it was missing or something,so what the hell can cause this? what can i look at?

i was thinking spark perhaps(plugs,wires?) or something to do with the fuel? or maybe the iacv? gimme ideas guys