Guys...have an 05 700 EFI that is my brother in laws. I asked around a few weeks ago about how bad it was running and tried everything that was brought up...still a dog. Here is what I have done:
Replaced Air Sensor....checked wiring...no issues
New Carb boot and air filter
New Plugs
New Fuel filter and gas

Still runs rough (1000 to 1100) rpm flux. When I pulled the plugs, left bank is good and grey, no soot. Right bank has a grey tip but black sooted base. Not soaked in gas as I would have expected since it just smells like it is running rich...

Anybody else have any ideas?

 

I've found most of the time its issues with the sensors harness than sensors(they dont usually go out) T-bap harness problems are the most common (repair kits are available) as well as wires rubbing on crank sensor harness at back of starter. this can cause rough running,spitting back,dying,etc.The wires are TOO thin,more like telephone wires and prone to chaffing. Had a problem on one 700 and turned out to be one strand of wire on crank sensor harness was intermittently touching starter,barely could see the abrasion! Also connectors and non noticable internal wire breakage can happen. I've only had to replace a couple sensors total since efi came out! Codes dont usually appear,you might try wiggling harness conections while running to see if you can notice a change in running. Most of the time its # 2875542 t-bap harness repair kit that is the solution. This may or may not be your problem? P.S if you still have Champion plugs,CHUNK em and replace with BPR7ES NGK. Plus check your plug wires and cap,can have issues there. Good luck OPT

 

You could also check for any sparking (shorting out to ground) by running it at night in a garage with all the lights out. Again move the wires and watch for small sparks that might show up. Sometimes the smallest spark can be detected this way. Be aware of carbonmonoxide and take precausions.

 

Polaris also sells an updated coil kit which routes the wires in a more direct direction...I know on my '05 700 EFI the wires come out of the coil and make a hard bend in the opposite direction...I haven't had any issues yet but I'm aware of that flaw and the T bap problem...

John