Concerning San Jose cars, the change seemed to occur in very late '65. The first carryover '66 GT350s (actually '65 cars with mid June as the latest sheet metal dates) have the humps with a flat floor mixed in. Just a very short time later, the flat floors only seem to show up on all of the cars.
So, at least in San Jose production, it would appear that the change over occurred in late '65.
I know that this has been discussed before, but on many of these late '65's (even with the hump), the rear parking brake cables are not routed over the frame rail. They are attached to the floor pan with unique brackets.