The speed controller can be wired any way you like to the motor without hurting anything. The only issue is it may run backwards. If it does, just reverse any two (of the 3) wires and it will run the other way.

I wouldn't recommend changing any lengths of wire from the SC to the motor or RX. I put an extension in my RX throttle lead once, and that gave the RX really bad jitters. Extra SC wire I think would also be bad to the motor. My stock Jeti wires are about 3 or 4 inches long. Extra wire in general is not a good thing, so try to keep every run short. No need to cut the stock lengths, but don't add extensions if you can help it.

I don't know if the Jeti has a programmable soft start. I use a Jeti SC on my e-sledge with the Nippy, and it's fine the way it is. I noticed with my Phoenix 10 as supplied, it was way too slow on the throttle up, so I disabled the soft start as per the Castle Creations directions, and it was much better.

Your JST connectors are good. Lots of folks are using them with no trouble around here.

That's great news Fire Medic. Welcome to the club.