First things first, you need to make sure you are running the latest software, firmware and bootblock. They can be found here
http://www.efilive.com/index.php?option=com_content&view=article&id=48&Itemid=133
Having a mismatch of software/firmware will cause issues, so it's really important to be running a suite of software that matches. The latest releases are:
EFILive V7.5.7 Build 180
EFILive V8.2.1 Build 170
FlashScan/AutoCal V2.07.22
You'll find a guide in our knowledge base on how to upgrade your software/firmware here.
http://support.efilive.com/kb_article.php?ref=7243-SFGL-2949
Brian (Tanc Crusher) has written a really good step by step guide from a user perspective on how to upgrade everything also, and how they all inter-relate. It was posted here and I think it may even be a sticky, but I'm not sure if it's being maintained on this site. It is being constantly updated on Diesel Place and is in the EFILive subforum as a sticky there if you need it.
Try connecting after that and see how you go. We have another knowledge base article on reading ECM/TCM/PCM's that you may find helpful if you are still having issues. You will find that here
http://support.efilive.com/kb_article.php?ref=8254-QOGC-9586
You've said you had problems with your TCM, but how did you go with your ECM? and can you perform other functions like read/clear codes?
Cheers
Cindy