I ride wet muddy sh*t and have no airbox cover....it's unnecessary!! If you're worried, you can get a pre screen that goes on in place of the cover to keep chunks of stuff out, but unless you're going through deep water, you'll be fine. Taking the cover off gives a lot of increase in power, so keep that in mind!!
It would help if you say where you're located because jetting depends not only on the mods you have but your temp and elevation. In eastern MA at average 400' above sea level on my blaster that I had the FMF, no airbox and a TwinAir filter (cleaned regularly to keep airflow the same), and the oil injection system I used between a 250 and a 290 IIRC. I'd start somewhere in that range. Also, raise your needle up a notch (put the clip one notch down).