I'm planning on taking my Secret Agent from 4000 (OOB) abralon to 1000 abralon. What differences should I see? I'm guessing that at 1000, it will react earlier. What else?
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Basically, yeah.  It's going to have an earlier arc type of reaction compared to the later, slightly more angular reaction you'd get from the 4000.  Considering how strong that cover is, I would only advise this if you're bowling on very oily lanes with tight backends.  Otherwise, you may find the ball will roll out.

I'd say, Go for it! Change it to 1000 grit since you have low revs and aiming for erlier roll. Dont forget to sand it against the track, not along the track. Im sure there are other ways of using the ball without changing the grit, stuffs like lowering speed, lowering your axis rotation and lowering your tilt if you know what I mean. However, life is full of trial and error, you wont know unless you experience it.