Picked up the bearings and seals for the 6-speed today. Big thanks to Paul Woods @ Woodsport for sharing the part numbers.

With these in hand, I can start assembling the gearbox
Installing the Hilux master cylinder was a breeze, about 15-20mins work tops.
It just needs a small tweak to the brake lines due to the lines connecting to the master horizontally, while the stock one is more 45 degrees in from the top. (shown below)
There is now more space between the tank on the master cylinder and my strut brace, so it's actually easier to get a bottle of fluid in there to top it up.
After the master cylinder install, I started looking into the electrical issue that forced me to bring the TrackDub home on a trailer a few weekends back. Now after having it start and run the other day, today it was back to just cranking and no firing... So I started pulling the loom out and it wasn't long before I found this.
Now it's not heat damage, as it's sitting above the gearbox, but something has pulled a lot of amps through that wire and melted it, and then it has corroded further and started shorting and causing issues. So just need to remove the rest of the loom now and I'll work on requiring the whole earth setup to some bigger gauge wire and try to see what circuits could have pulled all the power though it. Well I've run out of light in the driveway/garage today to keep working on wiring, so I might go back to working on this for a while.