We don't recommend installing a manual valve body on your Toyota 4Runner. The smog check program requires smog technicians' drive vehicles being inspected on the dynamometer while the transmission is in Drive gear (for automatic of course).
As far as the stalling during the smog test... we can only offer you information regarding how the dyno portion of the smog test functions; during 15mph 50% load is placed on the engine, during 25mph 25% load is placed on the engine. Ordinary street driving places less load on the engine then during the smog test. It's possible your Toyota 4Runner's transmission has a defective valve body. Repair/replace with a standard valve body only.