i was referring to the transmission connection plug in a previous post...not the access hole rubber plug in the bell.
that section of harness could have an issue causing one of the other intermittent problems.
the alternator..
did they perform the test correctly? i have had starters and alternators tested with printouts but they did the process incorrectly or used the wrong shit...so there is that. again there are several ways that can get burned. i tend to do that shit myself for that reason.
was it over charging like 17 v at higher rpm? seems it wasn't not charging and sucking the battery dead...or you would have mentioned that. it was 14 vin the vid you posted. revving up to 3-4k if it goes over 15 v is a clue.
overcharge will eventually murder the battery. ground and voltage feed issues can be a thing with that and can cause damage to ecm potentially...
you appear for sure have more than one issue. definitely would have to ohm the harness...and those harnesses suck to work with because the pcm is facing out and low on the drivers side. the way they are layed out is a pia...maybe the 99 is different then the 97-98 that way. dont remember specifics....its why i just robbed parts off of them building v8 swap harnesses...
the misfire codes...
Codes im getting are for "primary control circuit open/short"...for cylinders 4/5/6/8. One cylinder (4) on pass side bank, 3 on the drivers. For some reason cylinder 7 seems immune...despite its bank mates going crazy.
these seem to point to a branch feed or ground connection issue.
have had trans harnesses and o2 harnesses get pinched and fry stuff to a point and intermittent connections/corrosion wer cutting power to the injectors/maf/solo pak in trans ect...from hitting bumps or turning left or engine moving far from bad motor mount under wot.....
shit like that.
so. you can straight power / bypass power injectors and coils to eliminate a branch issue that will suck to dig out. if that eliminates the missing you know its a harness issue.
the bare wire you fixed is why i had concerns with the trans harness. have had those throw codes and cause misfire codes when they shorted. no blown fuse and codes they dont have anything to do with. f150 application but same shit...4.6 4r70.