yeah,even if you get genuine bearings and maybe even a heavy duty clutch i would only see it coming to around about $1000. Allow probably 3-4 hours labour to get gearbox out and back in and bout 1 hour max for clutch assembly inspection and bearing change.

Most front wheel drive cars dont have an input shaft/spiggot bearing as the input shaft is about half the size as ones in rear wheel drive boxes so the main bearing in the gearbox is enough in fwd to support the input shaft,no need for a spiggot bearing to support it....not certain if thats true for honda,but most fwd's it is....so its probably just your thrust bearing making noise (should always be changed when you change clutch anyway just to be safe. If it is the thrust bearing it will probably only be noisy when the clutch pedal is not push down (so that the clutch is engaged and there is load on the bearing)

Ask them to check your rear main engine seal while the gearbox is off and replace it if its leaking or shows signs of wear...saves taking box off again if it leaks later