Actually, the ECU just plugs in; it's probably the EASIEST part!
Pretty easy swap on an '01.
You need the ECU from an '03/04 manual V6 4WD Tacoma. Plugs right in and works properly.
4 wires from the clutch pedal switches to behind the glovebox to make the clutch start and cruise cancel switches work like they should.
The rear driveline will be a little short, but it will work. Ideally, a 1" spacer should be added. The front driveline will be too long, but it will also work.
The toughest part is drilling the firewall in just the right spots for the master cyl.
The '03/04 Tacoma didn't come with VCS/TRAC, so the new ECU won't support those systems. The VCS/TRAC ECU also controls the ABS- which controls your brake booster and speedo- so you need to keep that ECU. It's located where the new clutch pedal needs to go, and finding a spot to re-home it isn't the easiest task.
It's really like any other manual swap. When I say "pretty easy swap on an '01", I don't want to mislead you. I have no idea of your abilities, knowledge, tools, or workspace. I guess maybe it's not for the "average DIY'er". You definitely need to have access to EWD's, and understand how to interpret them.