gday Thommo you'll need to whip off all the old paint (paint stripper with a scraper, large buff with 40 grit pad, sandblasting etc) ALL the way to metal in order to access/remove all rust. treat rust and then etch primer, prime/filler primer and then paint. Might be worth getting your local sandblaster to do the battery tray. should be cheap and its easy to remove id imagine

Its a massive pain in the ass but it has to go back to metal if you want to do it right. the paint wholesaler i use reckon they have a good sealing product but im yet to try it