As for the tranny - you won't ever have to rebuild an SX tranny. You may have to "fix" it. I find the SX auto tranny indestructable and the gears are as beefy as any 350X gear - I guarantee that. The SX tranny failures seem to result from abuse such as holding the shift lever up to "clutch it" and then dumping it while gassing it. Another problem is people taking off in to high of a gear because they don't understand how an auto tranny works, this causes the SX tranny to jump out of gear and even one time that this happens, the wear begins. The shift drum seems to be a weak link, I'm not sure is the mechanism that holds the SX in gear is to blame but the drum is what suffers. I've seen a few bad grooves in the drum and the journal on the shift fork that rides in that groove gets ruined also. Then you begin to have problems. The other problem I've seen a few people do is the removal of the final drive output. It slides right out with just a few allen bolts and allows motor removal or drive shaft and rubber boot repairs. BUT, it also allows one teenie tiny thrust washer to get lost in the tranny during removal. The drive slides back in but soon first gear begins to pop out and later the real damage begins. Funny though, that washer floating around in the tranny never seems to jam up but rather the lack of it in it's proper place seems to start the damage.
As along as the oil is kept full then the SX tranny bearings will last forever and the only other problems are the one way clutches which if you change your oil and keep it full, they will last a lifetime also - IMO.
While on the oil subject and your motor rebuild question, a standard top end rebild can range quite a bit. If the oil doesn't get low then the cam and it's jopurnals in the head will be fine. Then simply a piston and ring and sometimes not even a bore job will keep the SX running smooth. But a lack of oil just like in the ever so desired "good journal" 350X head, will require a good replacement head. Piston kit is about 75$, valves are about 50$ for the pair with another 50$ to clean up the head and new valve seals etc. Ruin the cam and get an EBAY cam for 20$ or a Web cam for 150$. In time the cam chain does seem to stretch beyond the self adjuster and I think that puppy is about 70$ from Honda.
To me, I guess it all boils down to oil and abuse. The SX is a great motor and easy to keep running smooth. Most used tranny and motor
parts can fix your problem and are cheap on EBAY. I did a performance top end on my 85 motor sparing no cost and it was about 500$ to rebuild, thats a high comp piston, new valves, bore, web cam, cam chain and other misc
parts. I didn't even touch the lower end which is still stock.