I heard there's a way to water proof my distributor cap. has anyone here done it?
Dielectric grease worked on my old CJ's.
You don't have a distributor cap. Your engine (if it's the 4.0 in your user details) has EDIS (Electronic Distributorless Ignition System).
BAM! that just happened!
EDIT: You may also be getting your crank position sensor wet, and that could cause it........just a thought.
That is a common issue on old sensors actually. Water on the sensor can cause lots of issues if the casing has a small crack.
Try a new CKP sensor.