Before you know it, you'll be many hours into it and many more dollars. Your better bet may be to fix / swap in a new auto trans, then sell the car and just buy a clean low mileage TT. The money I have in my car over the past two years would have definitely bought me an immaculate factory TT with a few grand left over to spare (and saved me all the heartache / work). Just something to think about also.
93 2+2 Twin Turbo Track Build - jsworks.org for more info!