Does the 2nd gen have can bus and is that easy to program?

I don't know how much this will help. It may lead you to where you want to be though.

https://www.domi-works.com/collecti...ts/canformance-cantcu-transmission-controller

 

I would have done a few upgrades first before learning them the hard way. I would have installed a heavy 45lb flywheel like the one from Underdog Racing Development, fluid damped harmonic balancer like the one from Fluidamper because without these the syncromeshes rattle like crazy over 3500RPM. I would also have used a clutch friction disc from a diesel Toyota Hilux with a heavy pressure plate like the one from Underdog Racing Development from the beginning because I sheared the hub out of a stage 2 friction disc for URD after 22,000km. I think the part number is in my build thread. I also would have put an EGT gauge and KKK BV43 turbo on it before I burned a whole in number 3 piston on the first BHW engine after 50,000km. I think was lugging the engine for a few minutes between 2000 and 2500RPM. It is a lone story but I was on a road trip from Ontario and I had to get the truck shipped back to Ontario from Whitehorse, Yukon which was $6000 and 6000km. Since the second engine, larger turbo to reduce EGTs and EGT gauge to monitor them I have gotten 42,000km on the truck and it has been quite reliable.

I know you can buy standalone transmission controllers for some popular domestic transmissions.

TD Conversions https://tdconversions.com/ builds an adapter kit to bolt a TDI engine to the 4L Tacoma transmissions. They didn’t have one available when I did my swap otherwise I would have bought one.