The engine can be a 94-2002. That doesn't matter. Use your factory harness. Only thing is you may need to swap intake manifolds and a couple sensors and the intake manifold should be removed and fixed prior to install anyways.
You'll need a flywheel for a 360. Considering they weren't available with a manual in 1500s, you'll have to look at 2500 parts.
Also pcm programming is different between the 2 engines. They run each other "fine" as most would say but i don't find that good enough in my personal opinion. Since you bought a regular cab short bed 2wd with a 5spd and are asking about a larger engine.... I'm ASSUMING you're looking for the performance/hotrod aspect of it. Pardon me if I'm wrong. But, going on that assumption, don't bother swapping the pcm. Simply order a tune. You'll tell the tuner what engine and trans and you'll get a tune for that. The factory 318pcm fam be written for a 360. It's no more headache than finding the correct pcm, doesn't cost much more and really lets you benefit from the swap
