just bought a fmf...

This is what FMF recommends:

JETTING CENTER
We know how difficult jetting can be sometimes, that's why when we test our exhausts we also adjust the jetting to see what works best. Sometimes stock jetting works fine, other times a slight adjustment is needed. Here is what we've come up for in our area and is a great starting point for you as well. There are way too many variables in jetting to give you a recommendation that works perfect. Use these specs for a reference to help aid you with your specific bike. We developed these specs with a 32:1 fuel to oil mixing ratio of a 50/50 mix of race fuel and super unleaded, 0 - 1500 ft altitude at 70 degrees outside temperature.

JETTING INFORMATION:
Main Jet: 260
Pilot Jet: 32.5
Needle: STOCK
Needle Position: 3RD
Power Jet: N/A
Air Screw: 1.5
Fuel Screw: N/A
Comments: Remove airbox lid snorkel

FMF Racing - Jetting Center
 
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).