Stainless threaded rod can be be had in metric and standard sizes. It won't be quite as strong as the stock bolts but it should do the job. The european supplier where I got all the stainless hardware for my 750 project recommended the rod but I didn't want spend the $ at the time. The rod would be just slightly undersized but I doubt that would be much of an issue once things are torqued. The stock bolts don't fit snugly in the crankcase anyways. As to it messing up the alloy cases . . .the stock bolts are typically driven through with a hammer undoubtedly scuffing things up on the way . . .All this said, I would certainly straighten out the stock pieces, yours don't look to be beyond salvage. If looks matter, having the stock pieces cleaned up and plated would be an option.