I would guess there would be some changes. For one the 99 will be an OBD II system, and this would mean that the sensors and wire loom and computer might be different.
One way to deal with this would be to swap every thing over like the OBD II plug under the dash and perhaps even the instrument cluster.
You also might be able to put all of your sensors on to the new engine. The pitfall to the latter plan is that you might run afoul of the emissions laws. In CA, newer engines in older vehicles must have all the mandated emissions systems of the newer car, plus the smog referee has to approve of everything.
If the swap is done on an exact engine then no problems passing a smog check.
Also lets say you sell your truck before the next smog check and the buyer flunks the emissions test due to "tampering" The seller is then liable to restore the car to a legal position, That means you are on the hook for any issues discovered after the sale.
The industry phased in OBD-II in or around 1996. Vehicles prior had manufacturer specific diagnostic connectors and readouts. The code-reading tools were all different, how to access the codes was different, and what the codes meant were all over the place.
OBD-II standardized the connector, the codes and their meanings.
# ~1994: Motivated by a desire for a state-wide emissions testing program, the CARB issues the OBD-II specification and mandates that it be adopted for all cars sold in California starting in model year 1996 (see CCR Title 13 Section 1968.1 and 40 CFR Part 86 Section 86.094). The DTCs and connector suggested by the SAE are incorporated into this specification.
# 1996: The OBD-II specification is made mandatory for all cars sold in the United States.
Oh, yeah, the block and heads will be the same. You can even use a Taurus/Sable or Tempo/Topaz Vulcan. Just need to fiddle with the intake and accessories. The later models added the CKP and CPS, crankshaft and cam position sensors. Which means the timing chain, or front cover, may need to be changed, and the distributor replaced with the CPS stuff.
WILL A 1989 5SPD MANUAL TRANS WORK ON A 1992 3.0L BOTH ARE RANGERS.
I don't think it will work. I looked up the transmissions on fordspartgiant.com and a few other Ford parts websites and it seems as though Ford only offered a 5-speed Mazda M5OD-R1 unit for both new V-6 engines introduced in 1990. The 1989 Ranger V6 only offered a Mitsubishi FM unit. Hope this helps