96-00 only:
R150 = 2wd
R150F = 4wd
pre-96 R150/R150F not ideal! Different input shaft lengths, shifters might not line up with 3rd gens. The 4WD T-cases on these drop the opposite direction.
2WD manuals definitely exist. The kicker is that the bell housing from an R150 will make most R series transmissions fit.
I have an entire 5-speed swap for sale, but it has a transfer case/4wd, located in Southern CA. It's doable to use the R150F but I don't know about how compatible it would to change out the tail housing and eliminate the transfer case.
All in all, with a 2WD R150, swapping this to a manual will be even easier than the 4WD models. Technically you can use an R150F with the T-case and just not install any front driveshaft stuff, just leave it in 2HI basically. But hey, you'd get 2LO, which would be pretty awesome!
basically all you would need (The items I have for a full swap):
R150F 5-speed manual transmission w/ J shift transfer case (4wd only, you'd need an R150 if going 2wd)
Frame crossmember with transmission mount
Clutch fork
Clutch slave cylinder
Clutch lines
Clutch master cylinder
Manual brake and clutch pedal set
flywheel
clutch disk and pressure plate
throwout bearing
Front driveshaft (4wd only)
Rear driveshaft
Trans and T case shifters
Metal/rubber shift boot (under the leather one)
Interior trim with near perfect leather shift boot
Reverse switch
4wd diff switch (4wd only)
clutch start cancel switch (optional)
You would need all of that plus an ECU for 2000 4Runner 5VZ-FE 2WD M/T, and some flywheel bolts/misc hardware/fluids.