Given what you posted. 1st, take a cable off of the battery for a half hour, then reinstall. This should reset your car's system. Afterwards retry top.
If this doesn't do anything
You actually pulled the top, correct. You did the motor/pump, as well as new hydraulic lines. When doing this did you do the hinge lifters as well??? There are 4 sensers for the top which tie into the convertible controller. Two of these sensers are on the hinge lifters and two are located at the front of the top where it meets the windshield. These basically tell the convertible controller the location of the roof during movement. I strongly suspect an issue with either one or more of these sensers or the convertible controller itself. In that, your top isn't locking up at the windshield which strongly suggests that the convertible controller doesn't know the location of the roof.
You should consider using a code reader since these issues might have caused a code.