First of all, Welcome!
The wipers problem can be from a fuse at the panel, relay, intermittent relay, wiper motor, fluid pump, and even the column switch. Start with the easiest and work your way up. Many of your electrical gremlins may be due to clutch fluid running down the firewall from the clutch MC and down behind your fuse panel. If that's the case, you will have to solve that problem first or you will have constant fuse issues. This may be the culprit of your lighting issues also.
The brake handle cable will need to be spliced or found in a parts Comanche. Sometimes EBAY has them. I don't know if other trucks used the same assembly but some members have rigged them to work.
If your BA10 tranny needs repairs, don't put money into it. Upgrade to the AX15.
Read through the forums and you'll pick up a lot of great info. Ask questions. Post details and pictures of your MJ.
Be prepared to become addicted!