All 65 - 68 fastbacks have a drain hose as shown in the pics in the previous thread. If your car does not have them, you need to install some as the vents get a lot of water when it rains.
The other area I was suggeseting in the last thread is shown by the black proofcoat in this picture, this is the spot where the floors are usually not welded properly to the rear torque box.
http://s728.photobucket.com/albums/ww284/Downresto/68%20Paxton%20blown%20Mustang/?action=view¤t=Picture175.jpgI would say that installing the hoses will solve your problem.
The areas of concern in a Mustang are as follows,
Windshield & rear window seals leaking (possibly rear window seal as it is the rear floor getting wet, but amount of water you describe tells me it is the vent)
Trunk (bootlid) seal (unlikely as the trunk floor would have been wet & exhaust fumes entering)
Cowl vent leaking from rust or full of leaves (seems unlikely in your case as its the rear floor)
Heater core leaking (unlikely as you would have noticed before)
Door seals (unlikely as the wind noise would have alerted you)
Floor plugs or grommets missing or damaged ( you have already dismissed that one)
Drain hose from rear 1/4 vent is blocked (very commom on cars that have been stored outside) or missing (common on cars that have been accident damaged or restored) You stated above that the hose is missing.
Floor broken away from the rear torque box (most cars I have restored have had this problem) You can test this by removing the sealer around that join & levering slightly with a screwdriver, sometimes they are ok but sealer has moved or cracked. Reseal with good quality sealer.
