1960s 1966 Eldorado convertible top cylinder removal

[Julien Abrahams]

So, the Eldorado is getting to the point where it is driveable. The owner decided to put a new old stocl top on, before I had the chance to repair the top mechanism (motor etc.).
I ordered a rebuild kit for the motor, so that should be fine. I have already confirmed that the motor spins. So new seals should in theory be sufficient. Because there was still brake fluid in the system and I want to change to ATF, I wanted to removed the cylinders and flush them with brake cleaner. Let it dry for a couple of days and then fill the system with ATF. However, after removel the back seat and the trim on the side, I found that the cylinder is held in with two bolts at the bottom, and one that connects it to the convertible frame.
The inner bolt (closest to the rear seat) came out fine. The outer (closest to the sheet metal) will not budge. I think that maybe someone has already been in there and somewhat rounded off that bolt.
What to do now? Besideds flushing the cylinders I also want to install new hydraulic hoses (which have already been bought by the owner. Those aren't cheap at 100 dollars...).
I thought about removing the whole top, with frame and everything. But 1) I don't know if it can be removed with the cylidners still attached and 2) then I think I would need to compelely unbolt the top that has been recently installed which I do not feel comfortable doing.
Any help would be greatly appreciated.