TOPIC: 1962 Glasspar Seafair Sedan I/O project

I just picked this boat up a couple of weeks ago. I am new to the boat restoration. I have read a lot about these particular boats because I have wanted one for some time now. As I began to clean up the boat and started to really check it out I found the transom to be in bad shape (not too surprised). The floor is very solid so for now I am assuming the stringers are fiberglass due to the fact it's a 1962 with an I/O. The vin is 17XA2048. The wiring is also in need of updating as its a rats nest, I was able to turn it over before I pulled out the motor and out drive to begin the process of replacing the transom.
I have a ton of questions already. One is should I open the floor to put in a bilge pump area between the floor and the hull or leave it sealed? Two I noticed when I removed the motor and outdrive that they used a 1/2 spacer on the gimbal housing to get it to fit. So should I build my transom 1/2 thicker in the center to better fit my gimbal housing? Three is it better to go with an auto style fuse block or a toggle style fuse system when I rewire the boat? Four how long can I leave the wood exposed after sanding before I apply new varnish. Five what is a good epoxy besides the west system. There has to be a somewhat cheaper system that is just as good.
I have set up a photobucket account to keep up with my project.
s1152.photobucket.com/user/DeWayne_Partain/library/?sort=9&page=1

Any advice would be greatly appreciated.