For a while now, when the car sits running in neutral, there has been a little bit of a whine. When I press the clutch in, the whine slows down then stops. Pretty common signs of a bad throw out bearing. Recently the car has been grinding going into every gear. So, I've been babying it. Today was the first time in over 2 weeks that I v-tec'd the car, and when I pulled it from first, it wouldn't go into second, so I aimed for 3rd, it grinded a bit so I let off the pressure and waited for the rpms to drop and pushed again. It went in, but it was ROUGH and when I shifted to 4th, 5th, and 6th it was pretty rough. When I got on the off ramp I shifted into first and took off normal, but all the gears were still rough, just not as bad as when I shifted on the highway. Is this a bad clutch?

I just replaced the clutch master cylinder as it was leaking a bit and it helped my car to not grind every gear all the time, but you still can't shift gears at any rpm over 4k.
I have changed clutch fluid and ground the nipple off the slave cylinder rod.

 

A noise that slows down and stop is not a throwout bearing. It's a bad input shaft bearing in the transmission.

As far as rough/grinding all gears, you likely have a rusted spline:

 

I HAVE to drop the tranny for this...Don't I?

 

Yes.

 

Say I was changing my clutch and also wanted to change my input shaft bearing (My clucth makes the same whining noise when my clutch is out, but when its pressed in the noise goes away) is it alot of work to change the input shaft bearing once the tranny is dropped?

 

I have this problem as well, doesn't really bother me though. Does it matter?

 

Do you guys sometimes feel that the clutch gets stuck a bit though? Like say your coming to a light, and you push in the clutch it will feel like you didnt press the clutch in fast enough even though you did. Sorta like a delay..is this a rusty spline or more of a bearing issue? i think its my input shaft bearing because of the noise I hear.

 

That's the rusty spline issue!!!! My clutch sticks to the floor a little. I thought it was the nipple on the rod in the slave cylinder, but after grinding that off and greasing it up well, I found I have bigger issues.

YES it matters if you ever want to open the car up! When I go over 4k rpm, I can't shift. I have to wait for the rpm to drop back down to like 3.5 before I can pull the car into the next gear.
The noise isn't really an issue, it's just annoying.

My clutch squeaks a little too sometimes. I need to grease that fork better, but it's HARD to get to. With the tranny out, I'll be able to get it well.

Sure wish I could get rid of the rust through the bell housing hole....Without soaking my clutch that is.