1. "ground the blue data wire"
This test is only for once the module is actually programmed to the vehicle in the case that you would have trouble remote starting. It acts as a test to see if the unit is receiving the (-)G-w-R signal properly from the remote starter. (the connection should not be left to ground afterwords)
If the wiring was not correct on the first attempt to program the bypass module, would this cause it to not program when the wiring connections were corrected on any later attempts?
No, your fine. Only thing with some honda and acura, make sure to use the green connector at the ignition barrel, and not the white connector.
What can prevent the unit from programming, besides for connections, would be the following:
Constant ground on the ground-when-running wire. Remove this connection completely for sake of programming the easiest module to program.
Similar to previous, remove/cut the blue and white wires from the datalink connector. You don't need those.
Valet keys will usually not let the modules program correctly. Make sure to use a master key.
Similar to a Honda Accrod, put a charger on the vehicle. If the battery is weak, you may have difficulties programming.
Your connector should look something like this.