I have developed salt spray in the engine compartment of my 06RXP since installing the stage1 kit. I have ran it with and without the white plastic storage container. It seems to be on the front rear and top of motor!

Any Ideas?

Nothing in our Stage I Kit should be causing this. Have you changed your riding habits or location since modifying your RXP? Meaning are you riding more often, more aggressively or in a different location/conditions?

It seems as though the water is intruding through the seat seal being that you offered "the front rear and top of motor" are showing the salt residue.

Hopefully you're using a salt removal like Salt-Away when flushing and cleaning your craft!