I did, however, substitute the 9v battery for the stock Vex battery pack) and I'm having no trouble at all controlling the motors.
At least until the battery goes dead, which will be real soon.
Is the power isolated sufficiently from the signal lead in the Vex motor so that a power spike caused by a stuck wheel won't fry the port on the Arduino?
That depends on the motor wiring. You should be asking Vex that, not us.
on-board telemetry from a 3 axis accelerometer, temperature sensor, humidity sensorand Vex ultrasonic range finder
OK. What is this robot going to be doing? Opening and closing windows in a green house?