You may want to check around your window. Mine leaks on both sides at the bottom corners around the window and the water collects in the back where you are talking about. My top is about worn out though, just thought I'd try to help from one convertible owner to another. Also you may want to place some towels back there it helps. Good luck. 
__________________ 1998 GT Convertible
CAI, Bosch +4 Plugs & Fresh Wires,
MAC Pro-chamber o/r H-pipe & Flowmasters, no cats, 17 x 9 Polished Cobra R Replicas, Functional Rollcage (not style bar), FFRP 3.73 Gears, BBK Strut Tower Brace, Steeda Tri-Ax Shifter, fresh clutch, 180 thermostat, Monroe Sensa-trac shocks/struts, Steeda double hook clutch quadrant & adjustable cable, Steeda TA @ 15 degrees, Cobra front bumper, Cobra R 3" cowl hood w/ louvers, Smoked lights, HID 8K in headlights and fogs. | 
Water in back of my 2000 Mustang Convertible 
