so I figured it out and thought I would relay my findings for the next poor sod
First, the reason for the uneven lifting of the top
. When I removed the rear seat and inside quarter panels (the plastic piece that the seatbelts live in) I instantly saw that the lower mounting point for the driver side piston was unseated due to a nut that had backed off. When I would raise the top it had nothing to brace itself against to help lift the top.
Second, how to get out the Pistons!
To get out the pistons, the top has to be raised to allow access to the upper mouning point - the place where the top of the piston attaches to the roof frame in order to lift it. Once i raised the top it was really obvious.
Third, where was the hydraulic leak?
After taking everything apart and removing the pistons and motor from the car (as a unit) I inspected all seals for evidence of leaking. The driver side piston definately looked like it had let some fluid out around the shaft but I suspect this was due to being crooked when the lower mounting point came free. I checked the fluid level in the motor (pull out the little rubber stopper - the fluid should be level with the bottom of the hole) and found it to be about 50% lower than it should have been. I added the correct amount of fluid with a syringe and bled the system about 3 times. After putting the system back into the car and running the top up and down a few times there was no evidence of any of the components leaking so I think the fauty mounting was to blame, yahoo! Fixed! (I think, I hope
Bleeding the System:
this consists of holding the motor higher than the pistons and running them in and out about 4 times - check the fluid again and add more if necessary, add the fluid with the pistons retracted. I was told you can run the motor off any 12v power source but I just plugged it back into the car for simplicity. What type of fliud to use? Transmission fluid, specifically Motorcraft All purpose ATF XT-2-QDX if you can get it - or else any other ATF that meets that requirement.
Before you go tearing the car apart you will need Torx head bolts - the star shaped fittings - I would recommend gettting a set as I have used them in other places on the car (2000 Mustang Conv).
Feel free to PM me if anyone needs any further details on this