97 Civic Shakes and dies when slowing down and coming to a stop

My 97 Civic just started shaking today when I slow down and come to a stop. It died on me once as well, but drives fine when accelerating and driving around. When trying to restart it, it had a tough time at first but then started up and it was fine driving expect for the "D" light blinking when it was in gear. Then when putting it into park when arriving home, the gear switch still read "D" even though I had put it into park.

Any idea what this could be or how to fix it?

Also, we had really bad storms last night and upon going out to my car, I noticed there was water that leaked onto all the floors of all the seats, front and back. Any ideas on what this could be?

Any information would be very helpful!