Clutch
 

So I am going to replace my clutch, does anyone have any advice on what to replace while I have the transmission out?

any quality clutch kit will come with everything you need (pressure plate, disc, throwout bearing, pilot bearing), but while you are in there inspect the cable and fork pivot for damage, and if upgrading from the O.E. clutch to a high perf unit, i suggest replacing the quadrant with an aluminum piece, and installing a firewall adjuster. this should prevent any failures of the stock componants.

In addition to the above, check your U-joints for play. With the driveshaft off, you can also try wiggling the pinion flange to see how your pinion bearings are holding up. If your engine's rear main seal is leaking oil, this is the time to replace it.

Might as well have a look at your parking brake cables while you're there. They run above the driveshaft. They need to operate smoothly, just like the clutch cable.

I'd also consider changing the transmission fluid. You might enjoy a short-throw shifter, too (if you don't have one already).