Is the engine cutting out? You should be able to run the air box in the stock location without problems. Maybe you're not getting good airflow through the snorkel.

Im snorkeling mine next month and would like to know what you find out.

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well it idles fine but when i floor it it cuts out. than i took the filter out and it was fine.but on my snorkel i just ran it straight up so it shouldnt be much diff than stock.

 

Not sure what the issue could be, my 2011 s is snorkled and I'm running the stock filter and box with no issues. FYI, keep an eye on your spark arrestor if you are going to mud alot! Mine started running crappy at low rpm and it turned out the spark arrestor was coated inside with a layer of baked on mud!

 

I've had that problem too. I also was running the same setup with a k&n prefilter and outerware at the end of the snorkel and it ran rich. It added to the spark arrestor clogging up. soot plus mud. It wouldnt rev over 3000rpm because it was clogged so much. It doesnt take long either. Since then i've turned my intake snorkel under the roof so it doesnt get hit by rain and mud and pulled the prefiltering off. it seems to be much better.