[fuzzypuppy]

The guy at the shop has his best interest at heart $$$ not yours, I would call other shops and ask them about the repairs, getting second and third opinions/price quotes is always a good idea.
If this "shop guy" actually claimed that rebuilding your heads will hurt your bottom end I would not let him touch a skateboard, it's just not true, he is after your $$$.
you dont need to believe me though lke I said ask other shops or pose just that question to the board.
Now that said, if your rotating assembly "bottom end" was bad on it's own there would be signs of this such as, blowing alot of blue smoke out the exhaust all the time (bad rings), rod knock, etc, having your heads rebuilt would not change these problems one way or the other.
If your not mechanicaly inclined and don't wish to become such then you really need to find a trustworthy shop, ask family and friends, post your search on this board, there are good helpfull people on this board from all over, your last resort could be a dealership, not the best place for a person on a budget but at least they are certafied and you get a warranty.
I can't really comment on your problem anymore than that since you didn't post anymore on the exact nature of your "bad valve" or how it was diagnosed.
But I can say that if the same guy who fed you the line about a rebuilt top end hurting the bottom end was the one who diagnosed the "bad valve", then you definately need another opinion, you can post your symptoms here and give that a shot, but to get any type of diagnosis on here you'll have to get dirty and have some tools at hand since we can only direct you on how or where to test for a problem then give an opinion based on your results.
I will say there are some fairly sharp minds floating around this board,.
hope this is of help.