there are few shops that build costume cases..mountain mods is one of them. a lot of the old custom case builders have gone under the ones that are left make fan mods or heat sink mods now. if you have the cash you may want to look into a local cnc shop. most cases and atx cnc info is online. so you could have someone make custom parts for you if you have the cash then have them anodized like a paintball marker.
or have it Powder Coating.
Depending on what modifications you wanted you may find the best option is finding a local modder, discuss and plan the mod then buy the case and parts needed,
you may find modified Pc's on ebay or similar sites but they won't be exactly what you wanted,
Either mod the case yourself or find someone who can mod it for you, which will probably cost you
Find a local modder, pay for the bits, give him your idea, put him/her in a dark room with lots of sharp edged equipment, beer, crisps and switch on the electrics. After a few weeks check they are still alive and hey presto a modded case. Some charge ££, others just want permission to display work on web.
If it was someone like me then all it would cost you is the price of the parts, plus permission to post a build log, and maybe a sixpack to help the creative progress,
if you approach pro modders then yes it will cost serious money lol
the best thing is really to learn to mod yourself, it doesn't have to be complicated or expensive and you will get real satisfaction from doing it