I agree with Gene - let it dry out real good and see how solid it is when it's dry. If it's still solid and just discolored, then I'd coat it with something and then go back together, but do be sure you figure out where the leak is coming from and address that first (if you have not already done so).
If you get into cutting flooring out, you could be opening up a real can of worms and I'd hate to see you do that if it's not absolutely necessary.
Just my .02
-Greg
2017 Dodge Ram 2500 HD, 4x4, CCSB, 6.4L HEMI, Snow Chief, tow package.,1989 Skyline Layton model 75-2251.