The "D" handle issue is not in any way related to water in the trunk or locking module, treat the two separately.
The "D" handle has 2 rods connected to it that actuate the locking levers that lock the top frame to the windshield header.
One. or both of these rods have come loose.
Here's what you do :
Open the trunk and place the divider in the "top up" position. ( most trunk space )
Locate the rear bow latch ( just inside the top of the trunk opening ) and use a 6mm hex wrench to unlatch it ( counterclockwise )
prop the rear bow up with a screw driver placed in the locking slot up to the rear window bow frame.
This will provide enough slack in the top material so you can get your hands inside the header and feel the latching rods.
See if you can then finagle them to get the top unlatched. ( finagle is a technical term that translates to : "jerk stuff around and cuss a lot" )
Once you have it unlatched, you can remove the 2 panels and get to the workings.

As to water in the locking pump, dry it out and re-install sitting in a big plastic bag with tie wrap around the top.
Don't know what to advise on the water getting in there in the first place.