Why is the clock frozen

Yes, it's possible, although getting them all lined up correctly is tricky - if your rotation is off, one of them will dock and the other won't and things will wobble all over the place. I often use triple 1.25m docking ports for ship assembly in orbit.

I note that you can do this in the VAB, sort of; you can construct your ship like this:

|  |
|  |
V--V
X
^--^
|  |
|  |

where the ^ are upward-facing ports, the V are downward-facing ports, and the X is a connection between two of them. Only one set of ports will link up in the VAB, but if you load it onto the launchpad, it'll usually wobble briefly and then automatically dock the other port(s). This is particularly handy if you're designing something that you want to be able to launch in one piece, break apart in orbit, and connect back together later, but also want to use 2-, 3-, or 4-port connections.

Does the Ferram status window start saying "Minor Stalling Detected" at any point? I suspect that your wings are losing lift due to stalling, and if your wings are stalling, then your control surfaces are also likely stalling, which means they can't bite the wind to bring the plane back under control. Without video to see exactly what you're doing wrong, or how the plane is behaving, that's about all I can tell you.

With Ferram, you have to start out simple, and increment your designs. It's unforgiving in its realism, just like real aeronautical engineering. If you're having a lot of trouble with this type of thing, take a look at Scott Manley's videos on aircraft design (part 1, part 2, part 3). He shows how to improve inherent stability, among other things.