I too had this happen to my pylon bracket(although not as bad- sorry). I vacuumed up all the loose rust, and wire brushed what I could get to. I then painted it through the bilge pump access plate and though the engine area. I used one of those 'Turn rust to black primer' type of paints, then regular Rust-oleum. It has been 5-6 years now and I only get the occasional rust flakes now. It was soo bad before that my bilge pump was getting clogged, but I am not ready to tear my floor up ...yet!
-Rich
1990 Supra Mariah/351 PCM 1:23-1 PCM