Lowering the bike is fairly easy. Baron's makes a lowering kit that will lower the rear. You can lower the from accordingly by simply loosening the clamps on the triple key and sliding the fork tubes up. The Baron's kit for the rear includes a caliper relocation bracket.
As for the seat, I don't know anything about Mean City Cycles. We have a member here by the name of Rick Butler that does seat modifications also. If you contact him and explain your problem, he can tell you how he would remedy it.