In regards to cleaning out your engine I would definitely remove the gallery plugs. Also give the inside of the cases a scrub with a small wire brush as particles of blasting grit can become embedded in the aluminium. In general when you think you have done a really good job of cleaning the engine and got it as good as you can, have a cup of tea and then start the process all over again. Repeat a number of times, the grit hides everywhere and as already mentioned clean all threads thoroughly, grit loves threads. Check them with a bolt to see if it goes in easily without a gritty feel before assembly.
I stress caution because I have seen photos of a couple of CBX 1000 engine where all the grit was not removed, totally destroyed within a few miles.