I too have worked on my Cockpit Floor
I replaced my soft floor by removing the pedestal, then from underneath (accessed by port quarter berth, removing aft panel in port quarter berth and starboard cockpit locker... removed hot water heater and fuel tank)Now, that sounds like alot of removal of parts, but my hot water heater needed to be replaced anyway and my fuel tank leaked... replaced it when job was done. With all those things out of the way, you have very little space to work in, but its do-able. I cut away lower layers of fiberglass using a makita grinder. Did it in sections and used a pry bar to separate the glass and rotton wet wood from the upper layers. I did all this while my boat sat in the water in the slip. Plan on about 60 hours of work. I thought my damage was just one area but as I cut I found it reached the entire cockpit. The best condition fiberglass was the outside layers above, the underneath glass was badly deteriated and this is why I did not go at it from above (and since I was still in the slip). But with the boat out of the water and protected from the weather and rain, you might be able to go at it from the top. As far as epoxy injection... I think drying out the wood will be the problem here. I allowed several weeks for mine to dry out with all of the fiberglass removed from underneath with just the wood exposed and it never did dry out, even with space heaters used... so I decided to remove all wood and just reinstall new. I cut pieces of marine plywood and glassed each one in place with fiberglass chop mixture. When you expose this wood, you will see that hunter used pieces that were about 6x6 inches and smaller. When you are cutting new pieces, just cut them to a size that "fits" the contour of the floor. My pieces varied in size, but I cut them one a time and fitted and glassed them as I went along. Then I filled all gaps between the pieces of plywood (1/4 inch) with fiberglass chop mixture. Then sanded surface to get rid of high pionts and then laid up mat, roven and cloth in several layers until I had covered entire area. By using 1 foot by 2 foot sections, I could manage the task over head. I used plastic wrap to lay the glass in place and held and smoothed each piece out to get rid of any bubbles or excess resin and pulled the plastic wrap off when the piece seemed to be staying in place and before it started to kick. Over lapping each piece is important to ensure a good strong bond. Be careful which type of fiberglss resin you use, some have wax in them which require sanding between layers unless you can work fast enough to lay up next piece before the last cures. My cockpit has been finished for 1 1/2 years now and is very strong, very stiff. Feels like a concret patio.Good luck.David Underwood