This has only happened a hand full of times so far ,when riding through deep mud or muddy water
she starts to sputter with power loss ,almost like an engine skip but when I get out of the mud she's fine ,no problems on dry land.I tried using low gear and it made a small difference .
I also sealed up all electrical connections with dielectric grease ,still there .

any help will be appreciated .

I forgot It's a 03 400 4x4I auto with just over 400 miles,No mod's yet

 

One of two things. #1. Water getting into the air intake. #2. Water getting into the spark plug thru a crack or torn boot or cracked in the insulation. I would suspect the water in the intake. Don't get so deep.

 

jwoodsman, I have the same quad, HAD the same problem, first off how deep is the mud/water? Mine did it a few times then I started looking into it on some sites, and found the muffler on there 400's choke the engine basically, so I gutted the muffler and jetted it correctly for my altitude, and it hasnt sputtered since. I have had water coming just over my rack and it doesnt sputter.

 

The first time it started I was in just over the lights in water ,No water got into the air box .
most of the other times it's been over the tires ,I do some riding behind houses I'm worried about making it to loud by cutting out the baffles in the muffler .
It seems to only happen when under a heavy load .

 

Check the ignition system, check spark (should jump about 5/16 to 1/2" gap) and spark plug. How long since you replaced it, what does the tip look like? Brown or white? Does the plug wire have any checking. If so replace it.

 

I understand your concern about making it louder, first thing first, pull out your spark plug and check your spark plug color, it is probably a dark black, which means it is running rich, that could cause it also, if it is a tan color it is good.