"Here are the most apparent problems I'm noticing: 1) engine starts are inconsistent...sometimes it fires up instantly, and sometimes it turns over for several seconds before it goes."
Check the cold start injector time switch for the proper resistance. Cold start injectors are notorious for clogging up as well. When I pulled my injectors and had sent them to be ultrasonically cleaned, my cold start injector was damn near plugged.
"2) When the engine is cold, it idols at around 2000 rpms....when it gets warmed up it idols a little under 1000rpms and sort of dips down to 500 and back up repeatedly when I'm at a stop."
2000 RPM's on a cold motor is normal. Two main issues that will cause the engine to idle up and down at a stop: Idle speed adjusted too high (should be 750-850 RPM's at normal operating temperature) and a TPS out of adjustment.
A good cleaning of the throttle body is always big plus. The best way to clean the throttle body is to remove it from the intake plenum, remove the TPS sensor (the sensor is not totally sealed and can be damaged by the cleaner) get some throttle body or carb cleaner, clean the hell out of the butterfly and every vacuum orifice that you can find. Make sure to purchase a new gasket for the throttle body. The easiest way to adjust the TPS is with the throttle body off the intake plenum. Do the adjustment procedure before bolting it back on the intake.
TPS adjustment procedure
http://www.4crawler.com/4x4/CheapTricks/TPS/index.shtml
"3) I can hear some slight knocking in the mid rpm ranges...usually when I ease off the accelerator."
Do you know if this is motor related? Make sure your timing is set correctly. Timing advanced too far will cause knocking and pinging issues. An improperly functioning EGR can cause this these symptoms and a build up of carbon in the combustion chambers will do this as well.
"4) When I slowly roll over large bumps, I hear some pretty nasty squeaking...I'm thinking ball joints but I'm not sure."
Metal against rubber causes most sqeaks. Ball joints usually clunk when they go bad in my experience. Checked the control arm bushing and leaf springs. Sometimes you can narrow it down by spraying silicone spray on the questionable items. You'll know you found the culprit when the squeak goes away, but it will only be temporary.
"Again, these are just the immediately apparent issues. The previous owner was somewhat of a moron, but I think this is still a very promising truck despite years of deferred maintenance. I want to turn this into a smooth-running and reliable vehicle at first, and then I'd like to customize it and make it really sweet. "
Oh yeah, she’s got potential