Re: 1988 Bayliner Cobra 1800 restoration.
Sometimes ya gotta do what ya gotta do to get the job done. Cutting will get you where you need to be. Just save the piece, fleather the edges top and bottom and glass it back in. For the splash well, I would just paint, and not try to do gel coat unless you really want to. If you use a satin finish paint, the patched in part will not be as noticeable if its not a perfect job. Believe me, I know about not doing a perfect job. Perfect takes time and I want to use my boat. I work it until I say, "yep, I can live with that".
Every minute you spend working on it is one minute sooner it will be done. I found that even doing little jobs that take half an hour or so add up in the long run. It helps to have a work area where all the tools can be left out ready to go. Saves setup and cleanup time, which for me is a lot of time. I only do cleanup about once a week. I evaluate what tools and materials won't be needed for a while and put them away, do a cleanup, shop vac, and leave the work area clean for the next step.
Another thing I found helps a lot is to have a small piece of ply, about 2'x4' that gets laid across two trash cans and makes a great temporary/portable table I set up to paint on, glass on, mix on, etc.