Typically following what the manufacturer did is a safe bet, however, theres always room for improvement since they did what they could to meet the bare minimum requirements to keep costs down... 4x4s will work just fine... I decided to make my new engine mounts from plywood and through bolt them instead of lag screws... Definitely more work to glass in, but less likely to rot since any water can drain through the holes instead of sit there.
Same goes with floors, stringers, bulkheads, transoms, etc... put back what was there at a minimum, but don't be afraid to use something different or better... We'll tell you if its a good idea or not...
Typically exterior grade plywood is what most of us use for stringers, bulkheads, transoms, and floors cuz its readily available and significantly cheaper than "marine-grade" plywood, and basically the same stuff...
For now, worry about removing the rot and grinding down to clean glass...
Hopefully you're taking measurements of everything, more than you think you need, cuz you'll forget 3 months from now when you're putting stuff back together.
Good luck, stay cool, drink water (or coors light, same thing), and keep at it