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.