Have you verified TPS voltage to be over 3.7V at wide open throttle?
#29 is your VSS, any speedometer or cruise control issues that you have noticed?
#56 is TFT indeed, was the KOEO test run with engine hot or cold? If you did it cold try when she's warm (let her idle for a while, she'll warm up), if she was hot try when she's cold after sitting overngiht. TFT sensor is part of the solenoid pack and the general suggestion is to replace the entire solenoid pack. The sensor can also be bypassed thus "fixing" the transmission temp the computer sees - you need to be aware, however, that computer uses TFT as an input for adjusting line pressure, so if you bypass it and fix the temp reading at say 180F then the TCM will command line pressure corresponding to 180F even if the actual fluid temperature is -20F. If you are to do this, I'd suggest that you start thinking of your E4OD as a carbed engine with a lousy choke, and let he war up before you go anywhere.
#62 is the devil. How does your torque converter behave, do you notice the tachometer randomly jump up by a few hundred RPMs while you're in 3rd or OD? Did this code appear immediately after you swapped the transmission, or did you have some trouble-free miles for awhile and then she started acting up?
That last question actually applies to all the codes. TPS and VSS are one thing, but a bad solenoid pack can definitely give you the codes for the TFT sensor and the lockup clutch. Are you up for taking some resistance measurements at the harness?