seeking opinions on a 94 integra

I have a 1994 LS(i think) Integra, 119k miles, 5 speed manual.
Started hearing a knocking noise when I'm driving in low speeds, which
is gone by about 3rd gear.
I thought was the CV joints, because the boots were torn and had been for quite some time, and well, I've had this problem on another car and the sound was all too familiar. Took it into Mineke, got a diagnosis that the CV joints were bad, oh and by the way, I needed new brakes too.
Got a friend to help me replace the axles, which was a huge week long project, but it was finally finished. I did save some money having a friend do it which was cool, but I still heard that infuriating knocking! Friend said he thinks it's the wheel bearings. But he had so much trouble with the axels that he didn't wanna touch it. I didn't blame him really.
So, took it into the Acura dealership, as I am done screwing around with amateurs. $100 later I am told it is either the transmission or the clutch, and for $1000 for the labor costs ONLY, they'll tear apart my tranny and then tell me what the problem is. THEN they can fix it. YIKES!
Talked to a couple more people familiar with cars, described the knocking noise in low speeds. I did notice, however, that when the car is stopped and idiling, that the noise goes away when I put the clutch in. I also have noticed, that every once in awhile I have trouble putting it into first or reverse, but if I release the clutch and then press it again, it goes right into gear no problems. No problems with any other gears. New diagnosis: throwout bearing.
Now the argument is whether or not it'd be ok to have just the throwout bearing replaced, or replace the whole clutch. If that's even the issue...
My problem right now is strictly monetary and I'm looking for some insight as to how long these sort of things can go - and how to get the most out of it so that I can save up money and fix it - is it efficient to replace just the throwout bearing and if so how much would that cost, or just replace the whole clutch, and how much would THAT be.
Sorry for the ramble - any insight from experienced people would be greatly appreciated. Thank you very much!
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