Well, we know an extra driveshaft cant directly affect the electronics, so I would suspect some type of silly error somewhere. It is possible the ESC or some other electronics component has failed since the first run, but not very likely unless it was stressed its first run or connected improperly at some point. If you are certain all of your connections are secure, radio settings are correct and the calibration is done properly, the only way to know for sure is to replace the ESC/servo/receiver with a known-good unit one at a time until the problem goes away.

Rarely, some radios will seem to calibrate properly but have trouble similar to yours anyways. It may be worth trying a few things before you condemn any particular parts. One trick is to calibrate with the radio at max EPA, then try backing off 1-5%. Another is just the opposite, calibrate at a little less than max EPA, then turn it up a few extra degrees. I am not certain if some radios can "overextend" the throttle range or what, but I have seen this work in some cases.
Using the ESC programming card, I would recommend starting with the largest deadband (neutral range) setting, if you get clean and smooth operation you can increase this for better response. However, some radios "drift" a bit right around neutral and can cause some of the issues you described if the range is not high enough. Finally, I would suggest testing the truck in a wide open space where you can unplug the steering servo and check throttle operation. If you get normal operation with the servo not connected it may very well be a faulty or weak BEC in the ESC causing the erratic operation.