http://www.mustangmonthly.com/howto/34419/
I'm in the process, myself, of sticking in new floors, torque boxes, and frame rails on a '68 coupe... A '65 hardtop should be easier, since they didn't come with torque boxes from the factory.
Here's a Jeg's page for the connectors, should you decide to go that route, they will be less work, overall, and if the frame rails look fine, may be the cheaper way to go:
http://www.jegs.com/cgi-bin/ncommerc...63&prmenbr=361