Good Day,
Well, I can't say I have a large amount of manga at the comic store (Comic Cave) where I work, it is of various ages. In general, from my own buying experiance, I find that a comic store will either have lots of Lone Wolf and Cub and the first Viz/Eclipse comics (and these older stores simply didn't bother to try the new stuff) OR recent manga (tend to be younger stores). Some really large comic stores just have lots but this is just because they are big (although almost universally, the prices are not so good). In any event why don't you give us list and we will do our best to fill it. Our back issues are always at least 25% off guide (or cover price) and there are 3 Comic Caves here in Winnipeg where I can draw back issues from.
http://www.mbnet.mb.ca/~kthomas2/comic_cave.htm