So far, the clock has used a drop-in edge-mount SMA connector. Having built and sold a bunch of these, it is a tiny bit awkward that the power and antenna connections are on the side. The back would be better.
In addition, I've found an amplified patch antenna with a u.fl connector that would be a... not terrible choice for a built-in antenna, if one was going to be forced to use one (it works if you have it sitting in or near a window, for example, but not terribly well in the middle of a room).
Both of these are reasonably good arguments for trying a board with a u.FL jack mounted on the board instead of the SMA jack. You could bury the patch antenna inside the case somewhere if you wanted to go that way, or you could use an SMA pigtail and mount it anywhere on the back panel. If the antenna was internal, then the hole for the back panel could be a knock-out so that it wouldn't have to be used in that case.
As for the power jack, replacing the right-angle power jack with a vertical one is potentially an option. The jack is just a little more than a half an inch tall, which means that a square cut-out in the back panel the same size would likely be the best option for exposing it.