Don't pull or disconnect your old cable, yet. Just run this additional cable for testing. Hell, you could use household Romex cable for this test if you wanted or jumper cables clipped end-to-end.
Could be your feed cable connections are poor, a connector swage could be bad, or even a damaged portion.
Unless you're road course racing, I'd put the battery back in the engine bay. The effect of having it in the hatch on a street light to street light car is negligible.
I dont have with me something enought long to make that test but, here's new updates
Update:
Misfire happens when there is a voltage load so it's not just blower but can be an electric fan straight to the battery (it's in the trunk)
Tests #1: I've disconnected 3G alternator (regulator and stator disconnected) while leaving main feed on the stud.
Result Test #1: Start the car and no misfire
Test #2: I've disconnected 3G alternator (main feed on the stud) while leaving regulator and stator.
Result Test #2: Can't keep engine running. Electric fan trie to starts as soon as engine starts ASE with strange noise when it shouldnt and engine stops.
2 speed Electric fan is driven with a built-in volvo relay.
Power feed is on the alternator stud
Ground is to chassis
Switched 12v is from ignition switch
Trigger fan speed 1 is from PIN 27 (IAC1B) from Megasquirt
Trigger fan speed 2 is from PIN 31 (IAC2B) from Megasquirt
When disconnecting trigger harness, I can start the car and no misfire. I do understand I get a voltage feedback that I'm not suppose to but I'm not sure how to troubleshoot that one?!
Help would be appreciate.
Thanks,
Martin