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.