[Smidge]

Recently bought an 05 250x, and am trying to make the bike run as good as possible. It has the air box cut

air pump deleted

aftermarket exhaust (not sure what kind)

AP wire mod. 

Bike has a k&n filter but I want to change back to a foam filter, (maybe a no toil super flow kit)

I typically ride anywhere from 1500-4500 ft (socal)  elevation in 50-90° temps.

it currently has 130 Main

40 pilot

100 slow 68 starter

65 leak  

Needle clip 3rd position I believe.

According to Rick Ramsey's site most altitude adjustments are done with the needle clip, and fuel screw. But if I go up in altitude do I need to richen, or lean the jetting? And vice versa. 

On the mains the bigger the number the richer correct? 

I'm a total noob to carb tuning, all help is greatly appreciated

[Leardriver]

I would start with a 42 pilot and a 145 main jet. It take less than 10 minutes to change them, costs next to nothing, and that may be all that you need.

[Leardriver]

As you go up in altitude, the air is thinner and less dense. So, for any given volume of air, you need less fuel added in order to keep the bike at the ideal 13 to1 air/fuel ratio. At sea level, a 148 main jet, at 6000 feet, maybe a 142 main.

The pilot is somewhat of a jetting anomaly. It doesn't need to be leaned out as much, since the thinner air at higher altitude pulls less air through a given size jet. The needle clip and main jet setting is aided by the RPM of the motor slurping fuel through under pressure, where the pilot is only at play during starting, idle, and just off idle where the engine RPM isn't assisting in pulling fuel through as much.