Yes, cases SHOULD be kept as a matched set, Not impossible to find them, they seem to go for silly prices on feebay, but with so many people parting out Buells on here,,,, you should be able to get the parts you need at fair prices. I have a set of cases but they go to a frame, and a specific project. If you want pictures of anything,, let me know,
a used engine IS a gamble, I worked in a car wrecking yard for a while right out of high school. We had a saying,,,,
"It ran to the wreck" what you want to look for is lower mileage, well maintained, and a crashed bike. many times, there will be damages such as the primary cover, shifter levers, or timing cover damaged in the wreck, but you HAVE those parts sitting there.
I bought this spring for a friend a lightly used motor (XB12) that was in a wreck off of ebay for $595, the front cyl head mount was broken, so not good for another XB project without replacing that head, and the primary was gone,
BUT,, its going in a custom project that doesnt need the stock XB mounts. and to build up a motor to the stock XB specs would have cost him several thousand dollars, so he was very happy with the motor i bought off ebay. Yet i see some sellers trying to get almost that much for a set of cases. find out what caused the problem, and shop carefully, either rebuild what you have, but a used motor,, even at $1200-1500 might be the way to go.
OR,, heres a thought, buy a good used motor, and get back to riding, WHILE you rebuild your motor!