Before you get carried away and pull the motor...do yourself a favor and remove the air cleaner assembly and look at the rubber connector from the air cleaner to the throttle body. Any dust in it? Then remove the connector have someone hold the throttle pedal down and look through the throttle body. Any "mud" in it? When the dust and fuel from the injectors combine you'll find the throttle body, intake manifold and intake ports in the head all coated with a layer of "mud".
Remove the plugs and check them. Pull the spark plug wires off, then use carburetor cleaner and the little red tube to blast all the debris out of the plug port. Then use "canned air" for cleaning PC keyboards to blow the rest of the debris out of the plug port. I find it very helpful to pull the rubber collar out of the spark plug socket to get it down on the plug. If it hangs up, then you know you have more debris to clean out before removing the spark plug. You don't want that stuff falling into the combustion chamber.
IF you find "mud" in the intake tract then it has gotten into the cylinders and scored the walls ruining the piston ring seating. You may be able to hone the scoring out of the cylinders, but every motor is different. If badly scored do as someone suggested and get a big bore kit.
I have learned that even with a DFR sealed air cannister, if its really dusty out on the trail, inspect the intake tract every evening and be prepared to replace the air cleaner element frequently. I'm finding for a dry week in Moab I may go through several elements.
STURAT