On my AI programmer when two lights side-by-side flashed it meant you were half way between numbers.
So if light 3 and light 4 were both flashing your setting would be 3.5
Also - these bikes are not hyper-sensitive grenades ready to explode if you do the slightest things wrong.
Don't be afraid to experiment with your settings.
You have a slip-on muffler and some intake stuff done. Just like a million other people have.
Try their setting and see how it feels. Try somebody elses and see how that feels. Play with it.
I understand you want optimum performance and power as quickly as possible, but without taking bike to a dyno you're going to have to play around a bit to get there. Nobody can just tell you the perfect settings for your bike.
There's a million posts here on EFI settings. Find one that's posted by somebody with a setup that's really close to what you have and try it.
Then try somebody elses with a close setup.
A yosh pipe might be a little different than an FmF, but it's not SO different you'll destroy your motorcycle.
Changes in altitude, temperature, and humidity could play a bigger role than the difference between a yosh and a fmf.
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2008 WR250X
Gearing: 13t - 48t
Power Commander 5 / PC-V
Airbox Door Removed - Flapper glued - AIS removed
FmF Q4
Bridgestone Battlax BT-003rs