i'd take that residue off as soon as possible, it's a corrosion of some kind, it's gonna leave marks before long, at least it could. wipe it off with microfiber towels. the shells, if they're crank bearings, they should have marks similar to what's on the crank, you can match them at least to get some kind of close back to original places. if you've never rebuilt one of these motors, and you attempt to go the whole route of bore work, new pistons, bearings and chains, valve work, not to mention any carb work or adjustments, especially if you picked up this big from a different altitude, you might encounter difficulties in completing the finish project along the way. and assembling it then starting it and first few miles your motor seizes, you're going to be bummed. their almost as complicated as wrist watches. i'd suggest reassembling it with the old parts, unless something is broken, and do it very lightly. put it together clean, and then find out where your errors are. if you get it right and it runs, then you'll have some idea of what's going on with them for the cost of a gasket set and time. then try the rebuilt motor, it's gonna throw some curveballs of it's own at you.