There are a few fungicides that will work to remove any mold, mildew, or rot. I'd suggest to do some research and find out which are the most effective and cheapest. Concrobium is used by a lot of folks but the data sheets tell me it is TSP and sodium carbonate. Those are cheaper off the shelf as individual ingredients.
FWIW, when I restored my leaking Starcraft, I used bleach, soap, and water. I didn't have a huge mold problem but there was a lot of rotted and discolored wood. I haven't had any problems, since. Oxalic acid (wood bleach) that is found in many deck and fence cleaners does a good job of cleaning up wood, too.
When you have it all back together do a pressurized interior leak test. It will turn up even the smallest pinhole leak.