2001 Polaris Virage 700 Back Fire Issue

[Myself]

I just had a Polaris acting funny and found water in the e-box causing the problems.

[Policeman]

Backfire in the exhaust is ussually unburned fuel in the exhaust, that then gets ignited. About the only thing I can think of is intermitent spark.
I would try replacing the plug wires.

Thank you! I will try that next. Much appreciated.

[casey67]

Backfire in the exhaust is ussually unburned fuel in the exhaust, that then gets ignited. About the only thing I can think of is intermitent spark.
I would try replacing the plug wires.

[Policeman]

Scratching my head on where to look.

Ski was put away running fine. Pulled out of storage and needed fresh battery. Battery replaced.
It was running just a little rough but figured it was old fuel. Replaced, fuel and it became worse. Would start choked but would not go over 3000 rpm and ran rough.It began a series of start and run for a little bit and die. Figured it was in need of a tune up or the carburetor cleaned. I put new plugs (they were fouled), new fuel filter and put a carb kit in it and tried again. Now it runs but it is back firing out the exhaust as it does. I tried a carb that I had as a spare and it does the same thing. I did notice that the MFD was fading in and out last week with a full charged battery. It stopped doing that but I found no loose connections.
I realize there is a 100 things I should check but I feel like the problem keeps changing and don't want to go chasing my tail.

Any ideas where should I start looking first?

Thanks in advance!

Brad