What is involved with changing out the modules? For example, how long will it take, where can it be done, and can we change modules on the fly or do we have to transport all modules to one location first (like other ship components)?

Due to their size, the modules need to be swapped out at a location capable of that type of work, such as Cousin Crow's shops, and will require the ship to be there for a period of time. Exact timings are still to be determined but, due to the relative ease of access (remove lower cap then exchange module), this should not be a lengthy operation providing all the required parts are at that location.