V6 all four wires going into coil pack show 12 volts constant

So I swapped motors had car running but barely.. working with a remote tuner (through emails) sending him datalogs and he sends me back tunes… after having issues my tuner decided my stock maf was out of range (engine is stroked and cammed ect) so I bought and installed a hpx maf. After installing the new maf the car was starting but wouldent run for long and died. Turns out I had an aftermarket alarm that was distributing power and ground for the ignition system through a circuit board and doing who knows what with it. Believing that this must be the problem I carefully removed ever patch and splice and put all of fords wiring back together the way it was before alarm making sure not to mix up or leave anything to short out. This wasent the magic fix but car was still running so i figured i did good. After adding fuel and minusing fuel the cars afrs were not normal he decided to get help from another tuner. Finally I load this new tune from this tuner guru that taught my tuner everything he knows so I'm thinking this is gonna be good.! But the opposite happened I turned the key over and over no popping no nothing. When i checked the wires going into the coil pack for voltage i found something very peculiar. All four wires has 12 volts constant?! Was it always like that? I dont think so.. immediately I suspected the ecu. Luckily my tuner had one lieing around (we both use the same ecu which is how he tunes my car). Anyway plugged it in still the same problem. So I assumed it's the coil pack so I swapped that out …same problem. Here's where things get even more interesting. While replacing the coil pack and poking around with the volt meter I realized that when the plug is not plugged in to the coil pack only the power wire has 12 volts when I plug it in to the coil pack and back probe they all 4 have 12 volts today I replaced the wires from the 74 engine harness plug at the firewall to the coil pack same problem. My tuner thinks I made a mistake in the rewiring from the alarm but I went through each connection taking pictures and explaining all I did and he finally agrees it might not be my wiring. The only thing I didnt try is to bsckprobe and check for continuity from the wire starting at 104 pin connector all the way to the coil pack and that will eliminate the short distance of wires that go from 104 pin in the passenger footwell to the 74 pin in the passenger firewall (about a foot long). But I wont be surprised that everything checks out. At this point I'm kinda thinking the car thinks I'm trying to steal it and by towing the car to the dealership and have them flash my keys might solve the issue. Also I'm going to check my cam and crank sensors that they are normal..