STILL getting water inside spare tire are,right side only.have replaced ALL roof drains and no more leaks from them...but,still getting a puddle on right side behind wheel well from rain alone (and not much at that).anyone,anyone...Bueller...Bueller?
Have you done the process of elimination by using a garden hose and saturating one window at a time for a few minutes to see if any of your window seals are leaking? Is there water getting inside of MO when parked outside when it's raining? Is it only happening when driving while it's raining? Are you 100% certain it's clear water and not washer washer fluid dripping somewhere from the feed hose along its route from the engine compartment to the rear wiper) and maybe it's making its way to the spare tire area? I don't know off hand how that hose is routed. How are the tail light cavities? It takes about a minute to pop off a taillight to see if one side is wet or starting to rust due to water infiltration (probably unlikely, but might be worth a shot...) Is your hatch seal torn or detached anywhere that might allow water to trickle down into that area? Do you have a roof rack that might be letting in water?
If you haven't already, maybe wipe down everything thoroughly, then tape some papertowels on the inside walls of the spare tire space (but don't have them touching), then drive around in the rain (or do the garden hose thing) and then peek inside and see if anything is wet. It might reveal from which point the water is coming in, and you can work backwards from there.
EDIT: BTW, since you said you fixed drains and are still getting water... Does that mean that the water in the spare tire area is less than before since doing those fixes? Or are you saying the amount of water is still the same as before?