What about the dirt in the throttle body? How do I properly clean that out
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Yeah, that would have been the best thing to do for sure. Unfortunately the only thing that can be done now is deal with the here and now, hopefully it's not too bad.
You'll likely get many different opinions/advice on the matter, if it were me I'd try and track down exactly where the water came in since you mentioned that the snorkel didn't get submerged. Grab/twist all hose connections checking for tightness. It's possible that even while the snorkel wasn't underwater, the entire air box was for an extended amount of time.
Water was most definitely ingested into your engine, along with some sediment. I'd remove the entire air box and intake assembly to clean it off the vehicle, at this point you want to prevent anything else getting ingested into the engine. Stuff clean rags in the openings while the air box is off.
The throttle body will also likely need to be removed for cleaning.
After getting everything as clean as possible I'd plan on doing a few oil and filter changes (don't forget the DCT filter) to try and get as much water/sediment out of the system.
Say a Hail Mary, cross your fingers and hope there's no cylinder wall scoring. Then go ride! But make sure that all the snorkel connections are up to the job. If your snorkel isn't filtered, I'd consider modifying it so that it is. You can easily extend the snorkel up to the roof and put a pre-filter on it.
@CID links?