"Also best tool to make the cuts necessary? Reciprocating sawzall (I do not own one yet)? Will a jigsaw work?
Best tool for cutting the floor out?"
I had very good luck with one of these when did my gunnels from he top, you can adjust the depth and it cuts a curve very well, good luck!!
http://www.dremel.com/en-us/Tools/Pa...spx?catid=2101