Haven't been to an LCS for anything other than supplies since Heroes World at the Nassau Mall on Hempstead Tpk in the late 70s. So can't help with that part of it (except to suggest you carry at least some bags/boards).
But if you have any personal assets you want to protect, and you don't have a tax guy giving you advice, the simplest free advice I have is form an S corp (lower taxes for you assuming you make a profit).
And while keeping control of your costs will be a never ending pursuit, as others have already mentioned your best chance for survival is to have plenty of revenues coming in from multiple sources. But while diversified revenue streams are key, consider whether or not your MTG core concept and new (and back issue) comic books & TPBs becomes diluted or confused as you take on other logical related stuff like toys and licensed merchandise, Trek/B5 sci-fi collectibles, or collectibles like vinyl. Well organized store might let you squeeze in a bit extra without looking cluttered. Not knowing the LCS industry, this is just a general thought about concept dilution. Not a big deal, simply "cool stuff" can be a workable concept.
Definitely list back issues on ebay or send to MCS or something in your downtime.
.