I took my XT250 on a powerline trail near my house. I had been looking forward to finally ripping these trails I always noticed when I was driving past. It was a disaster that I will not attempt again. I kept pushing forward because going back seemed literally impossible. I got stuck in deep muddy water several times. I lost control numerous times but only properly crashing once though. I really think the fact that I got the bike home under its own power is a testament to the rock solid build of the XT250. 

I gave the bike a good rinse with a garden hose but it is still not happy. It was running as smooth as butter and now it's still running fine but the smoothness is gone. I plan to clean and lube the chain, the chain is in bad shape from all the mud and water. It also seems loose so I will tighten it a click or two to get it back in spec. What else should I be doing? I am really bummed I did this to my baby and I want to set things right as best I can.

Thanks so much for any tips, tricks, and suggestions!

I'm probably going against the grain of thought here, but i water blast my bikes. Sump guard off as gets packed above it. In my opinion its the only way to get it all off after conditions you're describing. Then pull the mag cover & wheels to dry out & also blast the brakes. Be as careful as you can not to get it in the wheel bearings washing the brakes if wheels off & washing in the brake drum, so try to protect them. Could pull the tank as get up under there. Firstly pull the air cleaner & block off the where it heads to the carb. Also the engine crankcase breather possibly goes into the airbox so might be easy to pull the hose & block it while blasting around the airbox. Block the fuel pipe while tank is off & flush a bit of fuel through the carb out the drain screw after your finished. If you wanted you could spray it over with some magic cleaner after the mud is off as they still look grubby when dry. So some sort of spray soap to them blast again. When dry its up to you what you do but i used to spray my old race bikes with a very oily twostroke mix then give it a wipe over. If ya saw my bikes you'd think i never clean them--but i used to lol, when in every weekend use. That my story but see what other say & do. Did ya get any pics of your ride--or too busy just surviving.

Stock tires are terrible off road. I swapped to DOT knobbies after my first ride. Huge difference.

Not sure why it's running bad now... fuel injected, etc... make sure water didn't get in plug boot or connections but first thing I'd probably check is if air filter somehow got wet... I think it's oiled paper or something and paper filters never recover after getting wet.

I just realized you're likely talking a Modern XT250. I'm 23 year behind--as usual.
Edit, Meant 43 year behind--thinking 1980 XT250.
& i read it as to 'how to clean your bike'--i dunno, no hope for me lol.
Does compression feel good on the kick start. Do they have a kickstart. Might have a built in valve lifting decomp for easy starting. Only reason i ask is if you've been buried in mud & overheating to the extreme, have the valve clearances closed up to zero. Unlikely with a modern motor id guess.Just trying to think why its running less than perfect & plug & aircleaner or airbox inlet restriction come to mind. Muffler internals not come loose & packing in there blocking it some.

  
Thanks Bill and Mark. I didn't take any pics on the ride but I did take one of the bike before I cleaned it off. The only reason the seat is clean is because all that mud went on me instead of the bike. The chain was not so lucky you will see. And yeah this was on my newest bike a '22.

Mark it isn't running bad really. If I never rode it before this ride I probably wouldn't even notice anything is amiss now. It just isn't quiet as smooth and elegant as it was. It shifts a tiny bit clunkier and just feels a slightly off. I wish I could describe it better than just 'less smooth' but that is all I can think of to describe it.

Thanks Mark for your suggestion. I will try replacing the air filter as that is cheap and within my wheel house complexity wise. I hope to avoid anything too complex as I am still very novice in the repairs department.

On the shifting, there is a sort of "linkage".  The pivot point of the shift lever can get gummed up and shifting gets bad.  Remove the allen bolt holding lever to frame, clean it and the hole in the lever.  Grease the pivot surface liberally with waterproof grease and reassemble.

I'd use loctite on the threads and/or check that bolt every ride to make sure it's tight.  Mine gummed up at an Endurofest and bolt actually fell out on the trail!  Luckily, we found it.  Didn't look like pivot had any grease from new.  With it greased and loctited (blue) it hasn't given me any more trouble...

here's a diagram:

  

Thanks for the pic. Looks like a nice model--under the mud.

Once you get your bike cleaned you can use Pig Spit Pso and your motorcycle will look brand new it’s made for bikes I have used it for over 20 years It’s the best