Quick question: I have read many post about the top not going up or down properly and how it is related to the hydraulic system. My top goes up and down but will not retract all the way into the body. My first though was that the rails are bent or outta whack, but could this be related to the cylinders as well. My first move should be to disconnect the cylinders and try the top manually ? thanks in advance.

Make sure there is nothing in the space where the top retracts.

It is possible you need to add more hydrolic fluid.