Sorry for your troubles. There is no reason someone shouldn't get 150k-200k miles out of a properly rebuilt 4L60E, and it doesn't have to cost an arm and a leg either. All anybody needs to know/do is here.
I can't answer the specifics of your A4 to M6 conversion, but as far as BIN files go, I always prefer to modify the one in the car. I once had a very well known tuner send me a mail-order tune and TCC never worked after that, with multiple attempts by him to fix it. I just wired in a switch and controlled it manually. Years later I finally reloaded the stock BIN and TCC worked perfectly. I copied over his tables and mods and finally everything worked right.
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