I'm gathering ideas, and cobbling togeather how-to's to change my knock sensor. As long as I'm going to have the IM off and the VC's are right there, I was wondering if there would be a good idea to replace the upper chain guides?

Looking at he FSM it appears that once you get the VC off the chain guides will be exposed, someone correct me if I'm wrong. Other than that I was thinking of changing the PCV valve, replacing the missing / broken rear Exhaust mani stud (#6 for thoes with a FSM), hopefully installing a Warpspeed y-pipe, cleaning and "cleaning up" the upper and lower IM's.

Anything else I should do while I'm there???

All that sounds like a fine way to ruin a weekend.....

VTC's if you have to, otherwise you are pretty much covered.
Don't forget coolant, you are going to have to remove the crossover pipe, so I guess you could do a T-stat if you wanted to since it would be easy to do with everything out of the way but meh.

Not much more I can think of

oh, vacuum lines if you haven't already, might as well, and at <$10 it's peace of mind

Soooo, Can I and should I replace the chain guides?

The most essential guide IMO is the one that the tensioners push on. These have the most load on them. I would inspect them, you will find grooves worn into the tensioner guide rail. If you fool with the chains etc. you should have a factory manual. If it were me, I probably would't fool with just the guide rails unless I was doing the whole timing set however if you see that a guide rail is shot then it wouldn't hurt anything as long as you know what you're doing.

Another suggestion I can add to the list if it hasn't been brought up already; Check all the heater hoses and bypass hoses. People largely ignore them and the little hoses the size of your pinky can cost you an engine. I've seen several engines overheated into oblivion because of those little guys. Of course they didn't have enough sense to stop before it was too late or were not paying attention to their temp. Good Luck!