2005 Mustang Convertible Leaking

I've had my 2005 mustang for close to a year now and never had problems with leaking until this month. There was almost a foot of water on the driver side rear footwell. I read it could be a drain hole and to park my car so the front is slanted down and now there is water in 2 spots on the driver side front. Not a puddle but still pretty bad. After it happened the 1st time I bought a water proof car cover which covered the entire car wheels and all front to back. After a week of rain which stopped last night i went to get an oil change this morning and the front driver footwell was soaking wet again. Nothing else was wet anywhere inside or outside, not a drop of water except the soaking wetness on the floor. The inside top is not wet at all, seats not wet at all, no other area of the floor is wet at all. The most confusing part is i have rubber floor mats and there is not a drop of water on top of the floor mat but soaking wet under. Where could it be coming from? The car has been in water before and this month is the 1st time i've had a problem with leaking. Even december it was in the rain perectly fine. I had a leak test done before i got the car and it was fine. I just had a basic inspection done today when i got oil changed and they didn't say anything in their routine inspection other than i need a new air filter (unless that can cause this problem)
 
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That is strange. The way I found the leak in my wife's Honda was to sit in the thing when it was raining. Hers was leaking at the door jam and running into the floor. Nothing was wet but the carpet on the passenger side.
 
I have an answer for anyone with a 2005-2009 leaking mustang convertible!!!

Ive had my dads old 2005 mustang convertible For close to 2 years now, and every time it rained I became puzzled on where the wetness of the rear floors was coming from, the roof wasn’t leaking neither was the windshield or rear window. I finally started doing some research and several forums and websites said it would leak from the rear window onto the rear seats, so I took my seat out and to my surprise water under both seats and my floor is soaked. So I got mad and disassembled the rear seats and quarter panel trim. I soaked the roof while also trying to look for leakage, and moved the hose to the rear quarter windows and behold the Mississippi river was flowing where my rear seats would be.

I then found the drain pouch that guides into the quarter panel, I noticed it was out of place and it’s hard to explain but if you disassemble your own car and look for a black pouch (just follow the exterior quarter window drain and look where it would go) anyway there is a tongue like flap that needs to be directed into the quarter panel drain and then soak with some light to medium pressure from the hose and check for leaks once all the leaks are gone the bad news comes. The drain pouches have to be readjusted every time the convertible top goes up and down.
This is my fix to water in the rear floor pan
 
I have a 2000 with a drainage problem as well. The water draining off the roof at the rear quarter window tracks on long the edge of the fabric towards the drain channels but ends up dripping off just outside of the rear of the channel. The result is the floor under the rear seat and foot well gets wet. anyone else with this issue? And to answer the first question I 'm always asked. Yes the drains are clear, not that that would affect how/why the water doesn't run off the roof fabric at the proper place anyway. Any ideas on a fix for that?