Welcome to the wonderful world of modern vehicle electronics.
Assuming the rebuild on the transmission was done correctly.
You need to understand the operation of the electronics controlling the transmission ( which I’m quite sure are quite extensive and is most likely the cause of your shifting issue(s) )
You could play swaptronics providing you have the funds available ( I would think that will get very expensive very quickly )
But a wiser path to take is to get a hold of a trouble shooting flow chart that covers the operation of the transmission and its control module(s) and follow the procedures.