mach1 motor in a ...

i would think its easier prolly to install it in 03. Because of distributerless ignision, and returnless fuel. Only big difference in A/T engine is UCU and it has Flex plate instead of flywheel(there might be some small bits that are different). 5speed trans itself will bolt up

So install it in 03. your fuel line will require very miner mod(if any). u might be able to use your harness with very small modification(i saw a website of this gut installed cobra engine in GT, and used stoock GT harness with simple modification to existing harness. can not remember what adress that was tho)
Or get harness along with ECU. U'll need ECU tho

Remenber, bolting engine in is easy part. hardest part of any engine swap is electrical part. So i would install engine to something closest to what it came off of so that at least electrical is similer