The guides themselves, or sleeves, I would go ahead and replace as well. - I'm looking at the parts fiche while I type this so give me a second...
Have you changed your oil since all of this has happened? Have you been able to take a peek at it and see if there are metal shavings in either the oil or the oil filter?
The oil pump is an internally driven gear set that connects to the clutch via the "engine oil pump drive". As that thing spins, it spins the oil pump, which is located behind the oil filter. If these aren't alingned - like, if he missed some shims or spacers or something, then your oil pump isn't actually pumping oil and the only thing getting lubricated would be the crank. And that makes sense because it sounds like you aren't getting any lubrication to the top end, which is where you said it was starting to discolor, right?
The good news we have had people on this site with more serious overheating conditions and they were able to resurrect the bike.
I would get eyeballs on the valve chain guides to make sure they haven't warped or deteriorated. You're going to need to really check that top end for any sign of damage or metal fatigue. Driving 20 miles or so with no oil pressure to the head isn't good. And it's not your fault. See if you can find out exactly what that guy did. If you need to, show him the parts breakdown...
http://www.ronayers.com/CLUTCH--C227893.aspx