I would think that there exists a good possiblity of developing leaks or worse by removing and replacing all of those engine tranny and primary bolts, even if they are done one at a time. But at least you would ensure that your fastners are torqued properly!
I would have similar concerns. Just what is the best way to go about changing out all the bolts?
Hot Toppers for me. Had em on my last bike and they held up perfectly year after year. I change bolts on things like foot pegs and stuff, but engine primary and tranny get toppers except derby cover which gets a chrome kit.