If you have bearing that are going bad, the chain will not fare too well. If you intend to have the carrier out and modify it make sure to put some new bearings in, im sure you probably know how to do that, especially if you ride in mud/water a lot. as for the chain not being lined up, does it move side to side any without the chain? If it does make sure that the axle nuts are tight on the brake side. Recently had the chain not line up problem on an 86 200x, my buddy who owns it had put in new carrier bearings, chain, sprockets, and rebuilt the rear bake caliper. Those have a small retainer clip on each side, the sprocket one was in place but the other side was not, so if he tried to slide of make a fast turn, the axle would slide outward and the chain would fly off (master link would fail first). As stated above somewhere, there is only 1 bolt that adjusts the chain, i recommend putting one on the other side, it will help in making sure the carrier is sitting evenly. On the topic of your rear brakes not working well, make sure there is not any water inside. I was riding an 82 200e in the mud and deep water (it was maybe 2 inches below the intake on the head pipe) and the brakes got full of water and the brake shoe material separated from the metal.
Currently : trx400fw, ct70, 250es,200x, xl80s, 350x, 350x, Trx250X,ALT185