What I did to my Comp to address the issue before I replaced the entire exhaust system from the risers back was as follows. I went to a local muffler shop and got a section of metal pipe in a diameter just smaller than the existing pipe that exits the hull. You have to cut out the bracket that is in the pipe and has the threaded bolt attached to it or cut off the threaded bolt flush or as close to flush as you feel comfortable. I then notched the smaller diameter pipe to allow it to fit over the bracket that is farther up the pipe so I could get a good bond and seal. I sealed it with 4200 adhesive and had allowed it to cure before I did the same with the section of pipe I got that was the same diameter as the 3 inch pipe coming out the hull. I sealed it with 4200 and allowed it to cure. Then I installed flappers and sealed them with 4200 both to the pipe and against the hull and tightened the hose clamp. The reason I elected to use 4200 was that I knew I was going to be taking this all apart within a year or two when I did my cap off restoration and I didn't want to have to deal with 5200. The "fix" I did I view as a temporary fix however, I no longer had my bilge running as frequently and my boat was drier than before the fix so I feel confident in my "patch" to buy me a few more seasons before I tore it all apart. If you follow my lead, I would also stick with the 4200 as you mention possibly installing new exhaust and the 4200 will seal it but also allow you to take it apart later on if needed.
'86 Comp TS6M - Reborn 2016
Riding a HO Sports CX Ski