800 skipping and check engine light HELP!

2011 800 50 inch and we just took the whole front end apart and took the whole belt system apart and put it all back together. Wellllll we get it all back together cranks and runs fine….so we think. Once you get up to 5 or 10 mph it starts skipping and cutting out and the check engine light comes on. Ive checked codes before but you cant check this one because the light will not stay on! I can play with it and get it to run about 20 before it starts skipping and i mean skipping pretty bad. I wouldnt think taking the front end or the belt system apart would do this but its just crazy it was running perfect then we take those apart put it back now it runs like crap. Any help will be appreciated.