My 700 quits running on trail after about 30 minutes of riding. I took to dealer replaced sensor and harness under seat. Did it again, replaced fuel filter and both injectors. Did it again, any suggestions???? It will start back up but runs rough and quits. After it sets for awhile it runs for awhile again like nothing was wrong.  

could be the ECM.  
the 2006 sportsman 700 has a recall for a defective ECM
seems they overheat and can cause a fire.
it sure sounds like your ecm overheating.
go to the link below to read about the recall.

http://www.cpsc.gov/cpscpub/prerel/prhtml08/08193.html  

I checked the recall, its not my model number. Any other suggestions? thanks  

it doesn't have to be the model number.
polaris used the same ecm for allof them, they only issued it for the model numbers they listed in an effort to issue the recall in a limited manner in hopes of not having to replace them all.

another one of polaris' many tricks to keep from having to pay for defects.

is your ecm getting warm or hot to the touch when it runs?
if so then you have a defective ecm.
if it is noticeably warm to the touch then it is getting too hot.
i have in the past gotten polaris to finally cover these under warranty by using a laser thermometer and recording the actual temperature of the ecm when the atv shuts down.

but be ready to wait and to be persistant with polaris as they like to take their time hoping that you will just go buy one instead of trying to get them to honor their warranty.