If I must.
When you re-silicone, obviously care must be taken (silicone in bearing seat, etc). Let’s assume that you did a PERFECT job and it’s ONLY in the groove, at the level you want it at (flush or ideally less than flush).
With few exceptions, a new silicone-based response (whether pads or flowable), will have a break-in period. The only thing to do is suffer through it. The closer your silicone gets to flush with the channel, the more naturally responsive it’s going to be (break-in period or otherwise), so you could apply it a bit recessed (or even more recessed if you’re already doing this to an extent) and see if that helps… but you’re going to have to break it in one way or another.
Be warned, though, if it’s “perfect” right out of the tube, that’s probably a sign that it’s been done wrong rather than right. If flowable plays perfectly with no break-in, it’s probably going to start to get slippy pretty quickly.
Regarding the rough bearing, nobody can say. We can say “sounds dirty still” until we’re blue in the face, but we have to take YOUR word for it that it’s as clean as it can get. If you are truly convinced you cleaned it to an ungodly level of clean and it’s still rough… get a new bearing! No amount of maintenance can fix a bum bearing. These are mass-produced commodity items, and there are going to be some bad ones. You might have a bad one. Replace it and save yourself all this headache!