You can try to bleed out the clutch hydraulic system with new brake fluid. Other than that, there's no other adjustments that could be made except under the clutch pedal. Check those two, anything more would mean parts need to be changed out (clutch, fork if bent, etc.). The hydraulic system is easy to work on, as I did a trans swap on my AE92. Just goes from the driver side firewall to the center, run over top around the trans to the front of the trans connecting to the slave cylinder.
Missing door skins, hope you mean the inside of the door? If inside (door panels), I wouldn't care much for a track car. Less weight

Outside, yea.... door from junkyard, SR5/ GTS are quite scarce. ESPECIALLY GTS. That includes your broken light and side mirror. Hey, I have POWER SIDE MIRRORS from a GTS if you want to buy them, I have a red set and a white set, with the switch. Let me know.
Shift knob, no problem! I have a pepboys one. It wobbled. I used electrical tape, wrap the top of the shaft to act as a spacer and slip the knob over it.
As for your shift changes, a fluid change is a first way to go. Just to let you know, the guy who designed the manual trans didn't really take into account longevity. 5 gear is popular to eventually pop out of gear on it's own. Grind 2nd or 3rd gear.
Besides the dirty dirty, rust is a number one problem. Common areas are around wheels, sunroof... from what I've seen, tho I have a rust hole in the trunk where the oem jack sits, on the fender at the bottom, and very small cancer spots around the windshield.
Aftermarket parts, not so much to get unlike a civic. JDM body parts, motor swap are more common due to lack of aftermarket stuff. There are a few stupid (IMO) body kits for the 2 doors. But I think the Levin front end with the factory skirts and wing looks good without overdoing.