Transmission rebuild, or misaligned clutch?
 

When my brother gave me his 93 accord MT, the car had trouble shifting, and a clutch pedal that would stick sometimes.

I changed the shifter bushings because the stick had (and still does have) a lot of play while in gear.
Also put in a new master cylinder, slave cylinder, and clutch hose. Ever since the pedal has worked properly, but still shifts hard.

I started to hear a noise at that point that i believed to be the throwout bearing;

While car is in neutral, and clutch pedal is out, I can hear a slight noise coming from the transmission side of the car. If I push the pedal to the floor, the noise goes away, and the engine goes Up maybe 25-40 RPMs. When I release the pedal, the noise comes back, and the engine goes Down 25-40 RPMs. When the engine has been warm, the RPM shift is not a noticeable as when it is cold.

So I had a friend help me put a new clutch in (flywheel, pressure plate, clutch plate, and throwout bearing) After starting it up, the noise was still there, just not as prominent, and the car shudders now when I engage first gear to get the car rolling.

I talked to a Honda mechanic that I trust, and she's convinced it's the TO bearing, because I didn't use an OEM TO bearing. And they have never had to do a MT rebuild in the entire time they have owned the shop. Later that day I mentioned it to a customer, and he's convinced that the clutch wasn't lined up properly.

There are some days where I can barely get the car to shift gears and I have to force the gear in, I've tried shifts at all RPMs and the only way it shifts smooth is when its below 1750 RPMs, and even then its no guarantee.

So I'm seeking some expertise from this fine board of people. If I have to get the trans rebuilt, I will. But if that's not the issue, I'd rather not.

Manual transmissions do fail on this board, but it is rare.

What aftermarket clutch kit did you install?

I would consider buying one from a junkyard with low miles. Check out car-part.com to search for one in your area to get an idea of the price. I would go for a junkyard one, because it is rare that manual transmissions fail.

I purchased the kit from Advanced Auto Parts; Perfection Clutch Kit (MU47701-1), Perfection Flywheel (50-21)

Something I forgot to mention in the first post;
The car spent about ten years in California before coming back to Massachusetts, and
when I got it the transmission was 1/2 a quart low (the passenger side axle seal leaks)
This car has done a full circle around our country and part of Canada

One more thing, when I push in the clutch pedal, there is a squeaking noise near the clutch fork.
not sure if that helps diagnose this problem