The Sunroof of my Atlas is leaking and water comes running down the center at the Rear View Mirror and then runs over the centre of the dashboard and down the radio panel.
It also has hard-shift from Park to Reverse or Drive and she literally jerks when I try to move the gearlever from Park to Reverse or Drive. This is so not normal!
Your sunroof drains are clogged -- I didn't buy an atlas with a sunroof, but I did have a beetle with one until last year, so I'll share how you can fix it. Your mileage may vary, and if you break it following anything I mention, its on you.
Take some plastic string from your trimmer (aka weedeater, weed whacker, etc...) and fish it down the drain holes in the sunroof (with the sunroof open). Don't force it.
I'd only do this IF the dealer tells you that its not covered by warranty.
As far as the transmission goes, take it in. I'm going to predict its some sort of valve body or shift solenoid issue, but that's purely a guess - without looking at your car it would be impossible to diagnose.