My 99 civic makes a metallic, rattle grindy noise from the base of the engine compartment. At idle the noise is minor but present, when the clutch is engaged it stops completely and under throttle it becomes significant. A mechanic has quoted this as a throw out bearing issue and wants to do an entire rebuild of the trans. I feel this is off a bit

Get a mechanic's stethoscope and listen yourself. Then, you may be able to better appraise what you think the problem is.

How many miles are on your Civic? Do you ever ride the clutch? Any signs of clutch slipping/grinding?

It may also be a broken spring on the clutch disc or pressure plate.

Bottom Line: If the tranmission needs to be removed, replace the clutch disc, pressure plate, and release bearing. A standard duty Perfection clutch assembly goes for around $100.

Yeah, should have mentioned, the car has 150k + miles on it. It had a brand new motor put in 20k ago along with a sports clutch, this is actually my roomates car, but he is a dip**** and can't do the homework himself. This morning he asked if I would taxi him back and forth to work and I said no because I drive an 04 pt cruiser that really is doing its best to roll a 7 right now. So instead of taxi-ing him I offered to suss out the problem with his civic