You want to get really, really fine sandpaper, wrap it around an Allen key or cleaning/in jamming rod, and sand the inside down so it matches the curvature of the BB.
For the nub, you'll still want one that's the same length as the patch, so the whole patch pushes down evenly, otherwise you may as well just use a normal hop.
Another thing, how smooth is the part where you removed the nub on the inside of the hop rubber? Mine wasn't very, although I tried really hard. To solve it, I also removed the fin (that makes the rubber only go on one way), twisted the rubber 90 degrees and then put it on.
For your hop, it may be worthwhile for you to do the TDC mod, although that'd require drilling a larger whole into the top of your barrel and having a screw poke out the top. It makes for easier adjustment on the go, and is apparently very stable and consistent, although I'm yet to try it.