Does anyone have their FFl and does not have a store. But just sells via catalogues to friends and word of mouth? If so, my question is - When the ATF comes out to inspect your "store" do they also check your own personal guns out? Or want to look inside your personal safe? Or want to look throughout your home? Or do they just want to inspect your books?

I'm not saying I have things to hide but  hypothetically speaking I really wouldn't want them checking out my camo cloths in my closet and my emergency food storage , not to mention some of the books I may have lying around may be on someones questionable list.

You have to have a section of your house set aside for the buisness part, and make no mistake about it you have to be in business for profit. Not to expand your collection, they will dump on you fast if you are just trying to use a FFL to expand your collection. They will make sure you are not violating any ordinance or law by having a home run business. You have to keep your guns separate from customer guns, they are not interested in your collection, only firearms on the disposition book. You do have to have a safe or alarm system to secure customer firearms .

BATFE maintains they have the right to search the entire premises for guns that are not on the bound book records.  If you have personal guns around, keep them on a separate set of disposition books.  If this is your home, it is technically "the store".

I will be selling to friends and word of mouth to make a profit. I will have a room set up as a store. I will not be stocking firearms, as I mentiond above I will be taking orders and ordering only what someone has paid for. My consern is my personal safe will be in the "store", does that make it fair game? What about a closet off of that room that is used as a cold storage of foods?

Its all fair game.  Just make sure your disposition records (bound book and 4473 forms) are in order.  Any "store" owned guns need to be in the bound book.  Any of "your" guns need to be in separate book.  

Thanks , I have my application all filled out and ready to mail. But I'm getting cold feet to whether or not I want my home searched or not. I am aware that with the patriot act they can do it anyways but I really don't want to invite them. Not that I have anything to hide, but the thought of an invasion of my privacy pisses me off.

I can understand the cold feet.  You are definitely giving up your 4th Amendment rights with a home-based FFL.  Good luck with your decision.  

Untill you get over this distrust of government accountants I would suggest you put this thought on hold.

I was told at my inspection any personal guns should be stored separatly or tagged personal gun not for sale.