I had this happen to me also. Pouring rain and I was on the freeway when the truck next to me hit a fairly deep puddle, sending a wall of water onto the Empulse.
When I got to work, the bike wouldn't turn off. Same symptoms. Fiddling with things in the dry parking garage, I found that very same connector and pulled it apart. Sure enough, there was a click and the bike turned off. I plugged it back in and the bike ran fine the rest of the day.
When I got home, I hit the plug halves with compressed air, sprayed everything with contact enhancer, and taped it all up with, you guessed it, gaffer's tape. (Great minds think alike!)
I figured the glitch was due to user error, since I had moved the connector down quite a bit from the factory position when I installed my LED lights, HID bulb with ballast, and garage door opener. I thought the new position exposed the connector more to the tsunami on the freeway than if it were tucked higher under the CF shroud.
After reading your post, I'm not so sure and I'll definitely pull it apart and add the dielectric grease, but I've had good look with sealing connectors with tape on other projects. I think you're good to go!
EDIT: I found this:
http://en.wikipedia.org/wiki/Silicone_grease#Dielectric_grease"Another common use of dielectric grease is on the rubber mating surfaces or gaskets of multi-pin electrical connectors used in automotive and marine engines. The grease again acts as a lubricant and a sealant on the nonconductive mating surfaces of the connector.
It is not recommended to be applied to the actual electrical conductive contacts of the connector because it could interfere with the electrical signals passing through the connector in cases where the contact pressure is very low.Products designed as electronic connector lubricants, on the other hand, should be applied to such connector contacts and can dramatically extend their useful life. Polyphenyl Ether, rather than silicone grease, is the active ingredient in some such connector lubricants."
Emphasis added.
But then, I also found this, which describes properties of the product I used on the connector:
http://store.caig.com/s.nl/ctype.KB/it.I/id.2014/KB.218/.fMaybe Adam or Protomech would like to weigh in...