Motor swap
 

I have a 98 ford ranger with the 2.5 and I am considering swapping my 2.5 to a 4.0, I know that I will have to get another transmission but will I have clearance issues getting the 4.0 to fit into the engine bay? Since it came stock with the 2.5. Any advice would be greatly appreciated!

No, no clearance issues

But its a "bad" swap
Changing engine sizes takes the same amount of labor and parts regardless of the size of the new engine, assuming it fits in engine bay of course, lol

You need:
the engine and transmission
engine/trans mounts, possibly driveshaft change
the computer and its engine wiring harness
radiator
exhaust system

Those are the main parts needed

Why the 2.5l to 4.0l is a bad swap is because you can just go out and buy a 4.0l Ranger factory built, so why waste the time and money making one?

A better swap is using a V8 from a 1996-2001 Explorer, same work, but in the end you have what Ford never built, a V8 Ranger, and its been done enough times that all the info needed is out there
There won't be alot of 2.5l to 4.0l info as far as wiring or other issues you may run into