My team had a problem with getting the motor to run backward so we switched the positive and negative wires. does anyone happen to know if that is allowed or if it will pass inspection?

This is perfectly acceptable. The inputs to the Victors have a set polarity. You can switch the wires on the output to get the direction right.

Yes. Wires with a non-constant polarity do not have to be color coded, <R54>

This is expected and perfectly legal. Inspectors will only look at the wire size and colors. At the output of Victors and Spikes there is no set rule for color as pointed out above. Hook up the outputs only to satisfy your design and motor direction.
The only exception is the compressor if you choose to use one. When connecting this to a Spike, follow the color code on the motor wiring (red to M+, Black to M-). The compressor runs in both directions but is much more efficient (less heat) running the correct way.