It is not the coil packs or ignition module. I replaced with a known working set and it still miss fires just like before. I also checked the MAF and it looks fine.

I have tested 3 of the connectors to injectors, to make sure a signal was being sent and they were fine. I ran out of time on my lunch break and will check the other 3 this afternoon.

Can you test a CPK to make sure it is functioning properly?

Can you check the EGR Valve as well?