The studs are very tough to remove without breaking. 500 cases are too small for 550 barrells or so I was told by a chap I sold some 550 cases to, he had made 550 barrels fit 500 cases by grinding the cases - I think, was a while ago now, at the time he was welding up mums car and I was more interested in getting shot of surpus parts and possible discounts. I suspect big bores might have been involved somewhere. I have dropped 600cc barrells into a 550 set of cases with the thought of putting together a cheap big bore engine but persued it no further as of yet, but they dropped right into place. I would expect everything to be pretty in line and accurate.
Last time I looked hard cb550 engines were cheaper than buying very many engine bits, but that was a while ago, I have enough engines to not look for any more, but before investing much more in yours I would look carefully what else might need work and consider a donor engine. It does sound odd to me for liners to be oval or out of line with each other.
