This is a 2001 Mustang V6 Convertible

Problem 1: Convertible top won't go up or down
Problem 1 Cause: Leak from hydraulic cylinder
Problem 1 Solution: Replaced both left and right cylinders (No hoses were mixed), bled the system with the cylinders removed from the sides, refilled reservoir with Mercon III fluid and placed the cylinder back.
YES IT WORKED
Until...

Problem 2: Convertible top won't go up or down
Problem 2 Possible Cause: Weak motor because it won't lift the cylinders that used to work
Problem 2 "Solution": After 3 bad motors (I repeat the same steps), I bought a BRAND NEW motor. I then removed the cylinders and drained ALL old Mercon III and replaced it with new Mercon III fluid. Bled the system and the cylinders work great when it isn't attached. I reattached the cylinders back and tested it out.
Didn't work.

Problem 3: Convertible top won't go up or down
Problem 3 Possible Cause: Mechanical Issues?
Problem 3 "Solution": Lube everything up including the top itself (the hinges of course)
Didn't work.

Now I'm asking for help. I did not replace the hoses because they don't have any leaks on them. The actual top (roof) worked well when I replaced the cylinders. I could also easily lift the top manually. The cylinders themselves seem fine. The motor is great so far. I checked underneath the steering to see if I blown out any [insert word that is at the tip of my tongue]. The batteries are fine. The motor is getting power, so I assume the relays are fine.

What do I do?

 

Maybe a clog in the hydraulic hose? Or a kink in the hydraulic hose? Not sure how you can test this without replacing the hoses one by one though. Sounds like everything else seems to be working.

 

The word at the tip of my tongue was "Fuse"

Another thing to note: I can easily manually open and close the top, but once I connect the cylinder to it, it's actually harder to open or close it. My logic is that I'm just helping the motor push/pull the top. It's going the right direction, but it's difficult even if I try to help it push/pull.

I'll go try and replace the relay next to the pump and see if that has any issue...

 

The hoses were fine before the cylinders started to leak. I followed the hose all the way as well to check for kinks.

 

I figured it out. I didn't see it coming since it was new, but it was the left hydraulic cylinder. The internal seal was defective. It was letting fluid out the other side whenever it's carrying a load.

Thanks for trying everyone.

 

A quick sketch in MS Paint if anyone was curious.