When I had my top hydraulics out for replacement I was able to manually open/close the top but I only did it a few times so to not damage anything.

Your best bet and probably most expensive would be to repair the entire system, which can be expensive. I hope your main lift rams are still there, those things are $1200 each! (the other are around 6-800....last I checked)

But if there is some way to get the roll bar/head rests to work correctly I would just rock it as a manual top.