I used ARTIC MX-4 thermal compound paste to insure I had good magnetic inductance to the sensors. I found it on Amazon. I had no issues when I replaced my drivers side main cylinder.
Like Pizza guy stated I had my car running and completed 6 manual cycles just to make sure. I completed my cycles with the top in the up position everything locked and shut. Then I had to add more fluid twice with just one cylinder replacement. I'd keep a close eye on the fluid levels. It is also easy to get the hydraulic lines backwards so just fruit for thought check to make sure they are all correctly located.
I would also double check the top control module to make sure the connection is good. With my limited time and trouble shooting with these tops I have seen everything that seems like can go wrong go wrong. From trunk latch sensors to cylinder leaks and everything in between you name it and it has happened. I have had to just take a step back and review all my actions or others actions from the fuse to the hydraulic lines. With the help of people on the forum and Top Hydraulics you tube videos I have figured it out and I have faith so will you.