Hey mabman
Have you got a cast 16" I love those haha
If the molded junction box is the culprit, just cut the cable before the mold and either hard wire it or make your own connectors.
An XLR plug & socket can do your power amongst many other heavy duty connections
You can use an 8-pin audio DIN plug & socket for your controller connections.
Total cost should be under or around $20
If you want to go hard out -->
Cost of new 8-pin power cable harness (controller to female 8pin) is $40USD and should come with another accessory 8 pin cable too. I ordered one and they gave me a 10AWG 1.2M power cable and a packet of circlips (the spring clip washers that hold the cable and freewheel etc. in place) oh yeah and it came with a spare freewheel too. I felt the price was worth it.
I would strongly suggest trying to re-wire before the molded plug because re-wiring the controller harness is an absolute bitch of a job and I do not wish it upon anyone haha. You won't have much fun making it external either, but if you really want to there is plenty of topics that have covered that if you do a search on the forum.
If you have the cast 16", IMO the internal controller had plenty of power to get it moving, mine pulled wheelies everywhere, and unless you put some serious volts through it you won't get it moving much faster with any other controller.
Good luck man !!