I'd say, whilst it's apart then get the crank balanced. It probably wasn't perfectly balanced in the first place. Having said that I've just fitted heavier pistons in my Guzzi without balancing, but; 1. It doesn't rev like a Ducati (on account of it's a tractor). 2. I didn't strip it down as far as removing the crank. 3. The gaskets/parts required for a rebuild are so cheap that if it shakes like a bastard, I'll strip it down and do it again. I did get my Monster crank balanced during the rebuild and it wasn't too pricey. As for the cases, I'd go with the 996 if everything fits (and they're in good nick) because they're newer, not been butchered and are stronger - IIRC one of the homologation mods included strengthening the cases due to racing failures caused by overstressing the smaller block.
Cheers dukedesmo yeah if a jobs worth doing and all that, I might well go down that route but I am on quite a tight budget, who does that and roughly how much would it cost.
I bottled out of doing the crank preload on my build as I didn't want to risk bolloxing it up! So I took it to Cornerspeed, he got the balancing done at the same time. Don't remember exactly how much the balance was but it wasn't overly expensive, certainly under £200 IIRC?