How to seal water leak?

[mpierce9]

After multiple tests I have identified a water leak from the engine compartment into the cab of my truck. The under the hood part of the heater assembly isn't sealed to the sheet metal well enough to keep water out when it rains. Water eventually ends up on the passenger side floor.

I'm looking for advice on how to seal this. I don't care to remove the heater box in order to accomplish this. Would RTV sealer + rubberized paint be a reasonable option?