Lifted Sienna electronic question...need a Toyota Guru expert opinion.

I am reaching out in this forum because there are quite a lot of Toyota guru's here. I have several Toyota's and one in paticular i have a question about is a 2006 Sienna AWD with a 3.5" lift in the front and 5" lift in the back. It has larger than stock all terrain tires and I want to change the final drive gear ratio. The Highlander from the same year has the exact same U151F transmission but with a lower final drive ratio. I swapped the Sienna U151F with a Highlander U151F and mechanically all was great. I got a code stating something about a torque converter lockup issue but everything seemed to function as it should. Long story short a friend of mine took the van on a road trip and it worked great most of the trip. They got home and it was acting funky like 2 clutch packs engaged at the same time. Nonetheless the transmission burned up.

I have since learned I needed to perform a computer reset, which I did not. So, the question is if I rebuild the Highlander transmission, reinstall the transmission and perform a computer reset will that fix the issue? Or can the computer be reflashed? I really would like to keep the Highlander final drive gear ratio if possible.

Thanks in advance for taking the time to read my post and contemplate my project!