In order for four cylinders not to be firing it would be two coil packs that are dead as each pack controls two cylinders. However I am confused as to if you have spark or not. You say it's not firing on one side then you say you have spark at all four of the cylinders then you question the coil pack. If you do indeed have spark, it's not the coil packs. If you don't have spark you could swap the coil packs from the old engine to test. One possibility would be pinched wires to the coild packs during install... if indeed the coil packs was out and reinstalled during engine swap.
1997 4.6 engine swap from hell please help
This is turning out to be the engine swap from hell. ive now replaced all the plugs leads and its not firing on the o/s bank not even 1 of them I have a spark going to all four plugs on that side as but i still have my misfire. coil pack maybe? could it be the injector wiring which to be honest i guessed them as i couldnt remeber how they went? or does anyone think the engine i got could be a dud? Ive had engine from this previous breakers before and they assured me this engine ran ok before they removed it. any ideas would be great 
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