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So I've got an 06 250x that won't start. We were out riding one day and it just all of a sudden died, and would not start back up again.(time before that when riding a couple times it randomly gave a single puff of smoke and a pop) Electric start works fine, but the kickstarter is extremely hard to kick. Has a ton of resistance.
-checked valves
-new plug
-cleaned carb top to bottom
-checked kill switch wires
-replaced ignition coil with known good coil
-checked compression, it was good.

Sorry for the delayed reply ....

I am thinking that part of the issue is the decompressor is not working , that is why it is hard to kick .... I am actually surprised the e-start starts it , if that is the case , but that would be my first guess .... next I would look at the timing .... check to see that the bike is still in time (is it rattling ?? , that would be a sign of a loose timing chain) ...... check all 3 marks to make sure it is in time , you need to remove the valve cover ... hand crank the engine (easier with the plug out) and get it till the cam lobes are facing the rear of the engine around 2 o'clock , then look for the marks on the cam gear to be lined up level with the case , then pull the large round cover on the clutch side , look for a triangle and a dot (dot on the gear) and make sure they are aligned , then the ignition cover small round plug , there should be a notch in the cover and a line on the crank ... they should all be aligned , if anything is off (most likely the cam marks to get the others aligned) then the chain is stretched , or possibly even jumped a tooth .....

That is where I would start my checking .... report back with findings ...