Re: OMC remote controls with the big red plug…

[Don]

OK, I think I understand now, you just have an engine side red plug that someone has cut most of the harness off, correct? In other words, you only have a few inches of wire harness bundle coming off the red plug.
Yes, you could certainly do a neat job of extending what is left of the harness leads using shrink tube/solder/crimp to make nice water tight connections. No need to extend the unused purple/tan/grey leads, just seal off the wire ends. Don’t chop up the original engine harness to use the leads, save it "just in case" like you mentioned. I think the wiring is 14gage, so you can just buy a few feet of red/black/yellow(for solenoid B+)/purple. I realize some of the same colored leads would be used twice, but you could always look back at the wiring before the splice to differentiate between the like colored leads.
Finally, there is no harm/problem in leaving both start safety switches in place. BUT, I think the control box safety switch makes/breaks the positive input to the solenoid, while the engine mounted safety switch makes/breaks the negative input to the solenoid. So, you would have a safety switch/circuit on both positive and negative inputs to the solenoid. In other words, don’t put both switches on the same lead, or you will have a direct short.
Finally, you will want to put a 20 amp fuse between the hot side of the solenoid (battery lead post) and the red/purple lead in the harness for safety.