It seems to me that if there is a hole in the roof near the front of the base and the elevator rod goes through that hole all the way up past the mast arms to that black hex cap which acts as a centering bearing. Looking at the manual and remembering what it looks like inside as I replaced the masts that hit a tree, your going to need the rod and everything but the masts and the bat wing. So all you should remove are two clevis pins and then pull out the masts and the elevating gear in the end of one of the masts.
A lot of work for no real benefit. I'd just leave the antenna down and not worry removing anything.
Just put a weather cap on the male "F" connector,if you are going to remove the antenna.