1999 355 convertible top problem, gummy fluid

Hey everyone. I recently had my convertible top get stuck halfway. I was able to get it to the closed position and began to bleed the system following Florida 355's thread. While following the instructions I found the old hydraulic fluid in the system to be gummy and in need of complete replacement. I was able to bleed most of the old fluid out by pulling the passenger side main piston and evacuating the old fluid through the bleed valve on the driver's side main piston, while sucking the new fluid into the system. My question is if I disconnect the hydraulic hoses from the main pistons, will I be able to use the pump with the emergency switches to evacuate the rest of the old fluid and suck the new fluid into the lines? Also, what is the procedure to get the main pistons back into balance? Right now the passenger side main piston is about halfway out while the driver's side is completely compressed and they are not moving in unison when operating the emergency up and down switches. Thanks in advance for any help or suggestions.