So I finally got a code for 1507 idle control failure which hopefully means you guys are right, so tomorrow I'll be picking up a different one. I really hope it solves the issue because I figured out the consistent 1&3 miss was because cylinder 1 injector was popped out of the rail a little I probabaly didn't completely seat it when I installed new o-rings, it's all good now though.
Ive known several people that did auto-manual swaps on their 93-01 subarus and every single one of them experienced idle issues and the car randomly dying. I dont remember if anyone remedied the situation but i know bansheeboy11 has some experience with this happening on two different cars. Most of the people got frustrated and dumped the car to get one with a factory 5spd
I've seen a similar issue when the switch in the transmission for neutral was faulty. The ECU didn't quite know when to engage its idle control. The clutch switch worked, so when the clutch was in, it knew to idle the engine, but when the clutch was out and trans in neutral, it sometimes had a hard time. Might also try testing that switch.
The pin is grounded, as I recall when I didn't have it grounded on accident it threw a code for the trans. I never had this stalling issue when the previous owner had the heads out of whack, now that everything seems to be right it's stalling. I'm pretty sure it might be the IACV like previously stated I'm hoping to be going to pick a used one up today or try and clean mine.
Welp tried cleaning my IACV and putting on a different one still stalls but doesn't seem as bad could also be that I'm looking for it now. Also now it only stalls under heavy braking, tomorrow I'll go through all the wiring and grounds again and everything else.
Thank you to everyone for the help and advicereally helped me figure this out and shocker the previous owner messed up the ground for the ecu when he manual swapped it. He put a connecter on the pin and it was too big to fully fit in the harness. So I pulled a the ground wire from a spare manual forester harnes I have( by the way, might be obvious to some but you can't use a forester harness on a 2.5 rs) to ground the pin and now it drives perfect, doesn't even drop past 700rpm. I can hopefully finally just drive it, and enjoy the 11:1 compression of the hybrid built engine.