New user here.... And really hoping for some help! First I have a 2001 SuperCrew 5.4 2V that I have rebuilt from bumper to bumper top to bottom all work has been completed myself. With that being said I will begin by explaining my blunder and the current situation it has caused. Recently while replacing the A/C compressor I put one of the bolts through the Starter Wiring Harness. That of course Melted the Negative battery post. I immediately replaced the harness from a donor truck I have. And bought a new battery. At first, it didn't seem as if any other damage had occurred. Then I started experiencing what seems like misfires. Then maybe transmission shudder, jerking, etc. I and several knowledgeable friends have bounced around several possibilities. All of which was not the issue. I have since narrowed it down to what I truly believe is an electrical short of some kind somewhere.
Here is what I've done so far and what I've found.
Replaced Starter Harness
Battery
And Trans Harness
Replaced Starter And Solenoid

Using my multi-meter I found a couple of circuits that with the Key-Off still showed 4.45 volts when they should not Circuits 20 & 21 of the Interior Fuse Panel. According to the owner's manual, those circuits have a couple of things in common. (I will include a pic of the descriptions) I have verified both with Key-On as well as Key-Off and the voltage doesn't. However, if I disconnect the Transmission Harness the voltage goes away.

PLEASE HELP!

 

If you noticed the heading of this sub-forum its dedicated to the Modular Motor V8 engines. For electrical issues post your question in that sub-forum---maybe get a different range of input or suggestions.