2005 CRF250R Jetting question

I've been a 2-stroker for the last 24 years and this 4-stroke is a whole new tuning experiment for me. 1st off, I've read about some of you taking the screen out of the air filter cage. What effect does that have on the jetting (leaner/richer)?
Also, I bought an aftermarket fuel (pilot) screw adjuster. The instructions with it say the exact opposite of the manual with respect to changing pilot jet to larger or smaller if you are too few or too many turns out. I'm currently about 3 1/8 turns out on the fuel screw. Should I go w/ a larger pilot jet or smaller? Will taking the screen off change the setting to the point that I should not change my current pilot until I've taken the screen out? Will it make me go more or fewer turns out on the screw?
I'm in eastern Massachusetts, hardly above sea-level. Temps about upper 40's/low 50's. Currently running 50/50 mix of pump and VP C12 race fuel. Stock header, FMF Q spark arrestor. I'm an A woods/enduro rider. With the screw at 3 1/8 turns out, and stock gearing, the acceleration is very smooth, no hiccups, no backfiring, etc. I want to make sure I have the right pilot so I am in the proper range of adjustability on the screw. FMF recommends going leaner on both the pilot and the main, but I wanted to clarify the conflict between the manual and the Zip-Ty adjuster screw instructions. Also a little nervous about going to leaner setting without any confidence in my 4-stroke jetting skills.
I appreciate any/all advice.
Thanks.

I rode today with only one change, removing the screen. My seat-of-the-pants evaluation found no difference whatsoever. Made no difference in the idle, off idle or mid-range power. I did not have the opportunity to get on the main jet at all today. Was riding tight woods, very wet with lots of leaves on the ground. Frankly, I think the motor is great the way it is, I just know that it needs a different pilot jet since I'm so far out on the screw. Being so far out tells me intuitively I should use a richer (bigger) pilot, yet FMF recommends a leaner (smaller) jet with the Q muffler. Am I wrong that being more than 3 turns out on the screw calls for richer (bigger) jet?