Hey there, behind the clutch there is another centrifical clutch, the problem is more than likely there. Make sure that there isn't anything going to get into the moving belt clutches, attach the ground lead to a good ground ( you should have had to disconnect it to remove the cover and put it out of the way of the moving pulleys) then make sure the quad is in neutral, start it up and give it some throttle and see if the belt pulleys are doing their thing. The pulley in the front should squeeze together and the larger one in the back should go apart to let the belt lower itself into it. If this is happening then hold the brake (someone to assist would be recommeded) and put it in gear then give it some throttle see if it also works the same way, if not or if it doesn't work as stated above then the centrifical clutch isn't working, if everything works that you can see then something may be wrong inside the trans itself. If it is the clutch behind the outer clutch then you may want to purchase a repair manual from your local dealer or online. I hope this helps alittle. Have a great week! Let us know what you find. And most of all good luck with your repairs I hope it is simple and easy.
Lar