OK, first get a set of bottle brushes.. I googled and got a set for about $5.. 3 sizes and bendable. Try just soap and water first go around. Then people use all kinds of cleaners. I have had good luck using vinegar and rice.. I put about a tablespoon of rice anf then fill the bottle up about 1/3'rd full and shake it.. that gets rid of a lot of crud. For rust stains on the glass try CLR, you can just soak the bottle in it. Also, for stains inside the bottle I break up some denture cleaning tabs and warm water.. that helps to.. you will end up using some of all of the methids depending on what the stains are. Also, a guy I meet a couple weeks ago said he pulls off a wad of SOS pads and bends a coat hanger into a hook and attaches the SOS piece for getting the inside clean.. that sounds like it would work!!
Good luck!!
MonkeyBoy