Where are you getting the other engine, sorry I made the assumption that you're getting it from a boneyard, but you might have a crate engine or one that's been rebuilt by someone.
I think that some Toyota throttle bodies have a cooling system, and I'm guessing that's the difference between the two. Does one have a couple of ports coming out of it and the other one does not? Also, it also could be some type of aftermarket modification like a throttle body spacer. Let me look into it and I'll post again in a few minutes.
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I got this from the Toyota NCF manual, you might have one of these.
A thermostat is installed in the throttle body. The thermostat uses the thermal expansion of the wax to open and close the valve to shut off the flow of warm coolant when the coolant temperature is high in the throttle body’s warm coolant passage. This prevents the throttle body temperature from rising more than the needed level, thus restraining the rise in the intake air temperature.
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Also, just reading some anecdotal chatter back and forth, looks like they quit doing the TB thermostat maybe sometime in 2003 ... so it's possible that it showed up in some 2004 model Tundras, but not in others. It also might have to do something with EPA emissions regs and they put it in on some but not on others. That's all I have for now on that actually, it sounds like they're interchangeable from a bolt-pattern perspective, but you might not have the correct modules to fully take advantage of a thermostat managed TB if didn't come from the factory that way on your truck.
That's just what I think makes the most sense. I mean, you can put all sorts of stuff on a throttle body and it still works, so adding in a different OEM throttle body should be pretty safe.