Crank, no start after bad plug wire arced

Was the #6 fuse actually which is cooling fan though I figured it may have other circuits tied in. The only code was 23 which I think was the ECTS but not sure I'm remembering right. Today I inspected around the steering column and found a black wire slightly thinner than the others which looked like the insulation had been partially melted away for about 4 inches so I replaced the damaged section and made sure no surrounding wires were exposed. Also around the same moment I noticed the harness located in the center console under the parking brake was slightly unplugged and once I plugged it back in and gave it another crank the sound was very different like stumbling or choking but not quite catching and the rpm hardly jumped at all. Also mine is all manual yet still has relays and fuses for the power options in place which begs the question, what are they providing power to? Oh yeah and before changing that #6 fuse the fuel pump was not running upon turning the key.

Maybe a timing issue or the other culprit that comes to mind would be the ICM. Now that I think about it when the crank changed it seemed like it's time had changed and for a minute there I thought it might start but still barely budged the RPMs. How can I check to see if the timing was thrown off? I just did the valve cover gasket as there was some oil in the plug wells and I thought it looked like the marks matched but I'm not sure I'm looking at the right marks. Another piece of info I have a multimeter and a fair understanding of electrical so I've tested all over and though the ICM gets 12v on the out blade the numbers read on the harness was something like.2.3 .4 and then 12.48 while the second harness was similar except no 12v and this was done with the key on.