ECM issues post JDM motor and transmission install

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I have a manual 2009 Subaru Impreza 2.5i that needed a new clutch and had a head gasket leak (lots of $ to repair). This was during the new (and used) car shortage, so I opted to have my engine replaced with a JDM and have a new clutch installed at the same time (by a master Toyota mechanic I know outside of a shop). On the test drive, the transmission blew (wouldn't come out of 5th gear). At that time, there were no transmissions available for the exact model, but the folks at Redline JDM in Ontario, CA said the transmission for the 2005-07 Legacy GT (6C-TY757VBBBB) would work for my car and would give me higher performance. I purchased the transmission (came with the associated rear differential), towed my car to a second mechanic master Toyota mechanic I know outside of a shop (1st mechanic passed away while he had my car), and had the transmission and rear differential installed.

My very first drive after the install(s) and I had two issues: 1) the car showed ABS lights and ABS felt wrong when I pressed the breaks (crunchy is how I describe it). The code read rear-right ABS sensor signal, which was also the same wheel the 2nd mechanic removed to replace the rear differential. We cleaned the sensors and the error returned. We replaced the rear-right sensor and the error returned. We replaced the breaks and rotors and no change. 2) the clutch would stay engaged when I shifted in high RPMs (4-5000RPMs) and there's a buzzy sound and a minor vibration (almost like a cable rubbing on something). I have since adjusted my shifting to avoid the sticking clutch.

Fast-forward to now and I want the car to drive correctly after all the work I had done and the effort I've spent trying to correct the warnings. My local Subaru dealer has now refused to work on my car since I told them I had the JDM parts and recommend I replace them with OEM parts. Well, that's not happening, since I've spent about $7400 between parts, labor, and diagnostic fees and it's more than the car was worth before.

Has anyone had a similar experience after JDM parts or know where to troubleshoot these issues next?

Thanks in advance!
 

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