I swear, man, you're gonna end up on the couch... good luck!
Is it the new head design or the old head design on the 99? I guess since you have the whole 93 around for parts swapping it'll work either way, but if it's the old head design on the 99 I'm pretty sure you can gain some horsepower by installing its intake manifold on the motor from the 93, then putting it back in the 99.
Also, maybe offer 300-500? He might take it, no sense dumping extra cash.
Determine where the smoke is coming from - if it has a blown front pump seal on the transmission or rusty trans cooler lines or a variety of other silly problems, you can spend less than a hundred bucks on parts (even assuming the transmission is shot and you pull the one from the 93) and new seals and fix it right up. Don't let on that you know what's wrong with it till the title is signed over, obviously. If the engine runs well but it seems to be going nowhere, it's probably a transmission issue, if the engine runs like crap you can put it back together using parts from your 93 as you already considered.