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Only difference that matters on flex fuel 3.0l engine is the fuel injectors
You should use the 1998 computer and wiring, so leave it as is
Take 2000 3.0l engine out, put the 1998 3.0l engines lower and upper intake with injectors on the 2000 engine
Put 2000 3.0l in the 1998 vehicle
That will solve injector issue, and 1998 wiring will be plug and play since its the same intake
You will also need to use the 1998 Cam sensor and synchro on the 2000 engine
1998 and earlier were 3 wire Cam sensors
1999 and up were 2 wire
Different types of sensors not interchangeable
2000 computer does have PATS, so if you use that computer in the 1998 you will have to deal with it.
If you want Flex Fuel then you would be best to get 1998 Flex Fuel Computer, you would then need the Fuel sensor from the 2000, by fuel filter
And you would still use 1998 intake but swap injectors only
Flex fuel engines did have different heads but obviously they work fine with gas only, or there would be no "flex", lol
And you can run E-85 using gas only heads with no issues, so not really a big deal either way.
The larger injectors on Flex fuel engines is because air:fuel ratio is different for gasoline and E-85, you need more E-85 injected, so injectors were larger to keep duty cycle in range.
Any fuel injection computer has to "know" the injector size(and fuel pressure) it is operating, i.e. when it opens one injector for 100milliseconds then XX grams of fuel will flow out of that injector.
Computer bases ALL it's Calculations on this, this is called the Fuel Trim
If you use wrong size injectors then computer will set Lean or Rich codes because its Calculations will be off, there is either too much or not enough fuel flowing out during that same 100ms
So you swap injectors to match computer you are using, your 1998 computer used standard gas only injectors