My car has 110,000 miles on it, and the engine was replaced 50,000 miles ago.

The first problem is with my 2nd gear, I'm having problems shifting into it, weither it's downshifting or upshifting. I already searched and found this, and one of the guys I work with suggested that I get it regeared because it is grinding while I try to shift.
The next is a rough idle, not only with the A/C on, but also when it's off, it does not continue if I start revving the engine, only when I let it idle at a red light.
Finally, there is a knocking, although my oil level is fine, and it has been changed recently and I was wondering if this solution would be recomended for me.
Edit: I replaced my reverse lights, and the fuse, but for some reason while I'm backing up, they aren't working, and ideas?

 

if the motor was replaced was the clutch, press plate, and throw out ber? MIGHT be the prob. how far from the floor is the pedal when you shift in other gears? if it's real low (1-2") it might just be the clutch assy. with that many miles it's prob the synch's in the mtx. you'll have to drop the mtx anyway to fix the prob unless you get lucky and it's the shift linkage. or you could learn how to rev match and change gears without the clutch pedal.

for your rev lights check to make sure the wires are hooked up to the rev switch on the mtx. the switch is on the top of the mtx, wires will be R/BL and B/W.

 

Unfortunately for me, my clutch is almost as tight as the day I bought the car

 

Not sure if this is your problem...
Have your tranny people check if the tranny needs some rebuilding hence... dog rings, syncro's etc.. Your problem may not lie with the clutch assyembly (pressure plate, throwout bearing, fork, etc.). Sounds to me like a second gear syncro.