I did something similar with my Gamefisher. I strongly recommend researching everything you can about stringer / transom / floor replacement. It's not easy, not cheap and mostly an itchy dirty messy job.
BUT, I can say in my case it was worth every bit of it. I spent a bunch of money ($2k+) on a $600 boat motor and trailer. And I am about to have to do half of it again. I will never be able to place a dollar value on the countless fishing trips Dad and I have made on that boat. Many would call it a pos and ugly but the fish don't care.
My recommendation, figure out what really needs to be done to make the boat safe and reliable. Do that, use it for a while and then think about what needs to be changed to suit you better. (thats where I am now) You'll know more about why things need to be setup differently and more importantly you'll get to enjoy it before tearing it apart. It's hard to complete a huge project like that, easier if you can remember why you're doing it. (just my 2 cents).
It took a very long time to go from here:
To here: