After extensive online forum reading, I finally figured out the TCU fault codes can't be cleared by the same equipment I have been using to clear the ECU/DME fault codes. So today I went over to Imola Motorsports to get the fault codes cleared. Within a few minutes I was able to take it for a test drive and cycle through all the gears. Victory! The paddle shifters on the steering wheel made it easy to bump up and down through the entire set. On the way home, I used all the gears, but the car was not accelerating or hitting any higher top speeds from before because the motor controller was still limiting the maximum current to the motor to 100Amps.
When I got home, I cranked up the motor controller settings and went out for a drive. I put the car in reverse, backed down the driveway and onto the road. I shifted into drive and hit the pedal, but the car went in reverse! This scared me a bit. I ended up driving the car in reverse back into the garage. After I got the car jacked up, I figured out the shift cable had come disconnected from the transmission mechanical shift input. So I hooked it back up and took the car for a spin.
With the new controller settings, the acceleration was a lot more zippy - more on par with my BMW 540i! I'm not squeling tires off the line yet, but I can get to crusing speed like you'd expect. I took the car on the freeway and took it up to 75mph, drove a few miles, then headed for home.
I'm super happy with the performance so far. It appears the limiting factor now is that the motor controller is cutting current to the motor when the battery pack voltage drops during acceleration, so the peak amperage being delivered is around 200Amps at the cut-off voltage. I'll have to re-evaluate the lowest allowable voltage threshold during high current draw so I can get more Amps to the motor to help with acceleration and top speed.
Here is a picture while going 70mph on the freeway.