Yes, 3.0l Flex and non-flex engines are the same.
2000 and earlier had an inline fuel sensor to "see" the ethanol content of incoming fuel, that was eliminated in 2001 and computer software was changed to "see" changes in power and exhaust to ID ethanol content.
Flex fuel engines needed and had larger injectors, ethanol(E85) requires more fuel to be added to get correct burn/power
If you are not going to run E85 fuel then you wouldn't need to change computer with engine, just swap injectors.
If computer is Flex fuel and pre-2001 then you would need the fuel sensor($650) with it or Check Engine Light(CEL) would be on all the time, although I believe there is a bypass for that, assuming you are stuck with a earlier flex fuel computer.
If you are buying the whole 1999 truck then selling that fuel sensor could cover some of the cost, although many just use a bypass when these fail.
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