2001 chrysler convertible top will not roll up only the windows

This might help. It's for a 2004 but 2nd generations are 2001-2006 so it should apply to yours. Typically, when when this happens, the system is low on fluid and/or must be bled. Here are the procedures: Lower the top to the full down position. Remove the rear seat cushion, seat back and inner quarter trim panels. Pull up sharply on the seat cushion at the front about midway between the middle of the seat and the outside edges. The seat back is held in by nuts. The quarter trim panels are held in by screws I think. Remove the cylinder mounting brackets and remove the cylinders from the trunnion pivot mounts. Rotate the cylinders 180 degrees (the hose fittings will now face to front of the vehicle. Disconnect the motor/pump retaining clips from the body. Rotate and raise the motor/pump assembly so the reservoir is in the up position. The rubber filler plug will be at the top. Raise motor/pump fitting to at least 2 inches above the horizontal rear seat back reinforcement. Tilt the motor/pump assembly to approximately the 10 o'clock position, with the rubber filler plug still at the top CAUTION: THE MOTOR/PUMP ASSEMBLY MUST REMAIN IN THE CURRENT POSITION UNTIL THE RUBBER FILLER PLUG IS REINSTALLED IN THE Step 12. Remove the rubber fill plug from reservoir. Fill the hydraulic system by adding Dexron 2 Automatic Transmission Fluid to the bottom of the fill hole CAUTION: DO NOT OPERATE THE TOP SWITCH IN THE UP (CLOSING THE TOP) DIRECTION. With two people, activate the top switch in the down (opening the top) position to fully retract the cylinder rods and hold for approximately 5 seconds, until the motor/pump stalls. A percolating or gurgle sound/feeling is an indication that the procedure is working. Top off the motor/pump with Dexron 2 and insert the filler plug. Install the motor/pump assembly into the vehicle mounting bracket. Rotate the cylinders back to the original position (hose fitting rearward) Install the motor/pump lead and hydraulic line clips (the hydraulic line clips are to assist in the production process) to ensure that the seat back/seat cushion do not pinch the lines. If the sticky side is no longer holding to the floor pan, the clips can be left off. Ensure that the bushing is still on the trunnion pivot mount and bracket. Tap the top switch in (raising the top) to get the cylinder trunnion onto the trunnion pivot mounts, if needed. Install cylinder mounting brackets. Raise and lower the top to ensure proper operation. Install the inner quarter panels, and the rear seat back and cushion. And Just a fair warning here - you WILL spill fluid inside your car. cover everything with garbage bags. Be careful and good luck.