200 KX-250 tuning issues....

Stock jetting is very close on this bike, FWIW.
The FMF pipe shouldn't change much. I would maybe go one or two steps down from stock on the pilot.
Maybe tak e the bike in for a leak-down test to check for a leaking clutch-side crank seal.
Here's a starting technique (cold) that never fails, with any bike..

Turn on gas
pull up choke
lean bike over until gas pukes out the overflow
put bike in 2nd gear, rock back and forth 7-10 times
don't touch the throttle
set at TDC and one kick should do it every time unless something is wrong.

This is out in left field, but if you've got a rich condition it'll get worse as the motor warms up. If you you are only fouling plugs after the bike has sat for a while, maybe you've got fuel getting past the petcock/float valve & "flooding" the crankcase. This could cause the symptoms you've described. You didn't mention what you are using for plugs either. There's a chance your choice of plug could have something to do with it. Or a weak spark.

The 2000 KX 250 was definitely a bit rich at lower throttle openings but you might take a look at your reeds before you start any jetting changes, the reeds go away pretty quickly on the KX.

I know there can be some regional differences on jetting but if the bike is still too rich on the bottom after looking at the reeds and you want to try something, here is what I have been running in southern California:

Needle: N3YF pos # 4
Main: 170
Pilot: (std)
Slide: (std)
Air Screw: 2-2.2 turns out depending on conditions
Fuel: Pump 92 , 32:1

I did not have a problem with fouling plugs but it was a bit rich on the very bottom, and seemed a bit lean around 1/8 throttle. To get the desired result I ended up 1 needle leaner (from an E to an F) and 1/2 a clip higher than stock (N3Y). I put in 2001 reeds which seemed to require the bigger main so you might not need to change the main if you have stock reeds.

Depending on how cold it is, I only have the choke on for about 5-15 seconds after I start the bike. After you start the bike, hold the bike at a high idle and turn off the choke as soon as it is warm enough to keep running. Continue to hold the bike at a high idle until you feel a slight temperature change in the radiator. Then clean it out by slowly opening the throttle and letting the RPMs increase until the bike starts to rev more freely. You will hear the engine noise change from kind of a loaded sound to a free revving sound. You will need to do this a couple of times probably, just be sure you open the throttle slowly so you don't inundate it with fuel and cold air. This process should blow any residual fuel out of the lower end. If none of that helps, you could try a hotter spark plug also… Good luck.

try looking really really close at the wetness on your plug and make sure it's not coolant from a leaky head gasket,, does your bike let out a pure white puff of smoke when you start it?

other than that you may be too rich on bottom, or have a leaky fuel inlet needle, or maybe your cylinder floods from hauling your bike. always turn off your gas peacock when you haul your bike.... is your carb floats level? or is the carb in tilted too far?

Tried a different oil?

A friend has a 2000 KX125 and had the exact problem you describe when he used Kawasaki Racing Oil. Switched to HP2, problem solved.

Good Luck.

Scott