Rough idle and stop when I first start the engine in the morning

In my shop, I bumped with several Subarus with the same first symptom. Usually, they are related to vacuum leaks, PCV valves, tumble generator valves, and fuel pressure regulator or fuel pump. Sometimes, MAF sensor. Every cause has its own characteristics that give us a lead to where to look. Gets easier using OBD2 real-time readings. Example: If there's a LOT of misfires, be suspicious of LEAKS or TGV (Tumble Generator Valves). If the engine stops when you press the gas pedal, MAF, or leaks.... And maybe the two issues may be related.

Since you disassembled your TB, the first thing you should do is hunt for leaks. No air can be admitted AFTER the MAF sensor. Start checking the tightenings, gaskets, everything you worked on. Then, give a good look at the intake air tube for rips or leaks. Check if ALL vacuum hoses are in the right position and if they are not torn. Check the very small hose with the L shape of the fuel pressure regulator (15 and 16 in the second image), check the brake assistance vacuum hose, and check the PCV valve. Subaru's PCV valve rarely fail.

Then, if the problem continues and you are absolutely sure no air is being admitted after the MAP sensor, you should then check both tumble generators. Start checking the wire. Then, check if they are moving using your OBD2 device. Try to read both at the same time, they should vary equally.

Anyway, I don't know if any of this will help you, because, when we talk about engines, there's a universe of things that can cause the exact same issue. I just pointed you the most common.