Evan,
There is very little current in the PWM cables so it really doesn't matter how long they are. Putting the controllers near the motors to cut down on the number of connections helps reliability. Are you adding tape to hold the connectors together? Another method is to secure the wiring with cable ties close enough to the connector that they cannot be pulled apart. If you are coming to IRI, find me and we can talk.
The West Mountain Radio Crimper is the best I have seen so far but the others are a close second. Another good crimper that I bought for myself at home (I have dies for RF connectors for various cables, I asked for this as a Christmas present) is available from High Sierra Communications on this page...
http://www.hamcq.com/coax-connectors...ax-connectors/
I recently bought the Power Pole die set but have not used it as of yet. When you look at the page you will see several crimp tools but I think two of them are the same and the price difference is the dies that are included. The coax cutter at the top of the page works nice on #6 wire (stranded) too.