Hi Dan, having come this far, it's not much more work to pull the bottom end apart and check all of your bearings...just for a little peace of mind and ensure that all is well down there. If they're visually good with no gross scratching or defects, check all of your shell bearing tolerances with plastigage (do a quick search on the site for more info on that), noting the colour coding on each one and where they are at in relation to the block and crank (and rod).
I haven't had a whole lot of experience with powder coating...had some XS cases done several years ago: not a bad finish, however they can be prone to off gassing during the heat/curing stage, causing defects in the finish. It still looked good, but not great. I'm not sure if this is a result of a lack of prep (the coating guy gave me advance warning that off gassing could happen, affecting outcomes), or the process. I don't know if there'd be any significant difference in durability, comparing to a good quality engine paint, but if done properly, the paint should give you a better chance at a better quality finish IMHO...(use a good quality spray gun and experiment a lot before shooting your cases, if planning on doing it yourself)....again, I'm not all that experienced with powder coating process. another consideration is the effect on heat dissipation that coatings may have, however with our climate up here I don't think that will really affect engine temps a whole lot. I believe that there are coatings that aid in heat dissipation as well, but I haven't done a whole lot of research into those, as I'm not into performance engine building. Going in another direction, you could go with Cerakoting, which uses a spray applied ceramic based coating product that is then cured in an oven....strong finish for applications with tight tolerances (popular with firearms)....intensive prep process involving very specific media IIRC...again, haven't done this, but would like to try. Similar to ceramic coating product used for exhausts. On the plus side, you have at least 6 months of our Canadian winter to work on your bike!