Hi Eagle
I've done some rebuilding of my scoot (newer than yours, but still...), including extensive upgrading & changing of wiring. What I have found is that the newer bikes use more multi-colored wiring - e.g. +12V power on mine is mostly orange, while newer use white w/orange stripe.
There is no easy way to convert between new and old, other than to lay down both wiring diagrams and work your way through them. On the wiring itself, I use masking tape and a pen to identify them.
When I did my previous re-build, I put in some standard connectors with silicone to waterproof them - they still work fine 10 years later. However, this winter I tried the new (to me) Deutsch connectors and they are highly recommended. Easy to assembe and disassemble (when you've made some mistakes) and seem very well protected from the environment.
Good luck.