light whirling or grinding while clutch is out in neutral sounds like input shaft bearing but when the pilot and throwout were bad it wasn’t making this noise all new kit with everything was installed now makes a quiet whirling grinding rotational noise when I press the clutch in it goes away , any help is appreciated

 

You may not have notices the input shaft bearing or it decided to make noise after you replaced the other parts . The whole gear set has to come out to get to the input shaft bearing so I can see how some may skip that part . I drove one with a bad input shaft bearing for many miles , it sounded like hell but never caused a problem

 

yeah it’s not loud like barely a difference but enough to notice it, also missing a mount bolt and a bell housing bolt can that hurt things?

 

Missing bolts certainly don't help . It leaves the other bolts under more stress and they should be installed . Get them from honda as they may not be standard or metric . Honda has their own thing going on .

 

Honda bolts are all metric to the JIS standard. Nothing strange going on here.