Yes, you can, just swap the '01 upper and lower intake to the '07 engine so '01 wiring will match, flex fuel or gas only matters but as far as injector size, so if '01 computer is Flex Fuel then use the '01 injectors, it doesn't matter that you will never run ethanol, the injector size is what computer uses to calculate the amount of fuel that will be released when it is open, larger injectors(needed for ethanol) release too much fuel for a gas only computer so you will get Rich code and CEL will be on all the time.
Look at the accessories, where alternator, power steering, AC and pulleys are located, also see if fan belt for 2001 and 2007 are the same.
If they are the same then fine, but if there are differences I would swap the brackets around, you can use the newer parts but on the older brackets.
That way when you go to get a new fan belt in 5 years 2001 belt will fit.
You will need to get parts for '07 3.0l engine when changing things like front and rear main seals, which I would do when engine is out, also oil pan gaskets are year specific.