Hey guys...thanks for the imput. I went and checked to see if the rubber hose was connected, and it was. The only thing is that it wasn't a rubber hose, but a thin plastic one that I noticed was kinked where it came out and bent along the firewall. I figured that was as the problem, but when I disconnected the hose from the cowl drain I didn't notice any water in there that might have been backed up from last week. Nonetheless, I went and replaced it with 1/2" heater hose that slipped on nice and didn't kink. Before slipping it on I put a pipe cleaner through the drain and it didn't appear clogged.
Now, I have attached some pics I just took showing the vent door closed. It looks to off alignment somewhat on the passenger side (see pics). I noticed when I had taken the cowl vent assembly out that there were 2 sets of bolts I had to take out on each side, besides the main armature in the middle for the lever. Each side to seem to have two small arms connected by the two bolts that went through long slots on each arm to allow adjustment, I asssume. Would these be the connectors that adjust each side of the vent, and is this why the vent door isn't sitting straight?
Also, in one of the pics (with the vent open) you can see that the corner of the vent opening some of the rubber gasket seems to be lifting slightly. How would I fix this so that I wouldn't have to pull the gasket all off and do it all over again?