You likely get to keep TOD if you only replace the engine. The TOD works off of the transfer case which is married to the transmission. Having TOD without the stock transmission/transfer case is close to impossible to expect. You have to keep in mind that TOD is just Isuzu branding for an early traction control system. As far as a TH400 bolting up, I don't know. I have an intense personal hatred for automatics I do believe however that someone on this forum was looking into what would bolt up and doing a little more than talking about it so you might try searching a little more. Also, read this so you don't get your hopes up:

Originally Posted by AutoPros
Have a '99 that one of our customers wanted to remove the poor running 3.5L for a more popular motor to source parts for. Bring on the GM Performance 5.3L E-ROD! GM 4L60-E Transmission! GM Performance Supermatic Controller! Advance Adapters to Jeep Dana 300 Transfer Case! Retain A/C, Power Steering, 4WD, pretty much everything other than TOD. Still in fab process, but will update with photos as the progress continues.