I couldn't remember the idle spec on the KLX250S.. Mine always idles at 1300 - but I have 11 motorcycles and get "mixed up" sometimes on coughing up specs..lol

 

Ok, yes the manual has it at 1.2k. Right now it's very jerky in 1st at that idle speed,much smoother at 2k but maybe I need to tune the air fuel mix screw

 

Ahh, yes, it looks like you still have issues with the pilot system - hopefully just the fuel screw setting.. Or, worse, a clogged pilot jet, pilot air jet, etc..
This must get fixed. You won't know how well the bike performs until it's carb is functioning correctly.. MCM could very well make the problem worse as it "taxes" the carb more than stock timings..

 

I'll adjust it ASAP. I still think I'm going to need to do the mcm.

That spring you are talking about... Is that part of the mcm mod? Or a separate mod

 

When you start researching/learning about the MCM, you'll learn that you have to deactivate/remove/reposition the ACR(Automatic Compression Release) . It is pressed onto the end of the exhaust cam..

The easiest thing to do is to deactivate it by removing its' spring - very simple, very easy, 10 seconds and your done with ACR issues..