An update almost 2 years later. The AFI TBI in my FJ40 continues to run very consistently and well. I have had the truck to 12,500' (Tincup Pass) and it ran well (albeit down on power). I started the truck at 20F and it started just fine. Starts just as well at 90F, which always taxed my carburetor. I bought their legacy kit (not the new OBDII one) and upgraded to their modified FJ62 distributor for another $295. I also bought the 48" harness so that I could put the ECU in the glove box. I left the timing and idle speed at AFI's recommended settings. When I tried to adjust either, I got very poor results.
Overall 'perceived power' is very good - when you floor the truck at 60, it's soon going 70. It may not have more actual horsepower, but it feels a lot more responsive and more like a modern engine. I 'lug tested' it and at about 500 rpm on my tach, it just shuts down. You can't lug the engine any slower than that. I could lug the carburetor to about 400.
Two things that bug me: when you start it cold, about 45 seconds into the warmup cycle, it misses slightly (while idling in the driveway). It always done this, every time. Not really a problem, but it seems out of place in the EFI world. The 2nd thing is that if you upshift too soon while driving (or don't downshift going around a corner in town), it will bog rather obviously. I don't know if this is a programming issue, elevation issue, or a physical issue (like the size of the throttle body). The solution is just to run it to higher RPMs in each gear. If you do this, it tears up the road with glee. So, some driver cooperation is needed.
For the price ($1300 back then) and effort, it has turned my truck from a cantankerous/dangerous thing into a turn-key driver and simply more fun to bomb around in, without worrying about hot soak and stumbling, etc. I am no longer 'that guy' with carb issues on offroad runs.
I would love to drive a Holly Sniper setup, since that's the new hot babe on the block, but I can't say I'm unhappy with the AFI setup.
Steve