Do you have catalytic converters on it?

It'll smell like raw exhaust no matter what if they are gone. I wouldn't assume it's running rich just yet.
I'd be curious to see what your fuel pressure looks like at high RPM under load. Being able to rev past 3k in neutral but not under a load suggests to me that it may not have adequate fuel. Just something to look at, the Ranger fuel pump is plenty capable of supplying a stock V8 - maybe a weak pump or partially clogged filter? Kinked fuel line? I kinked one on my V8 swap and it took me years to find it but it didn't really cause any major issues.
My opinion on the computer/rev limiter deal is that if it came out of a manual trans donor vehicle, it doesn't matter what manual you put behind the engine... the computer doesn't look at the transmission for anything other than the speed sensor on the speedometer cable and maybe the neutral switch (not sure on that.) Otherwise as far as it's concerned, you could have a direct drive to the rear axle with no gears or a 4 speed or a 5 speed or a 10 speed from a semi... It would not know that you exchanged one manual for a different manual.
It might be worth getting a scan tool that can view live data from your computer if you rule out the other stuff we mentioned. Using an OBD-1 computer narrows your choices down a bit but the Bosch 1300/Actron 9690 have some rudimentary ability to do that. Might be a few others out there too. I have an old OTC System 2000 scanner that will show live data but only in the moment, no graphing.