How to fix whatever I did wrong with my new station...

[Hakuryu]

The tug.

Hard to see, but the tug is about 1.5K from the orange fuel 'arm', and 3.9k away from the station core.

Issue #1 - Switching craft with the '[' works fine to switch between the tank and the tug, but if you switch to the station it blows up. BOOM! Station pieces flying everywhere. Have to go to the space center and select the station; does not blow up if I do it this way. Is this an issue with the 2k draw/relevant distance? Only 4 struts on my station, and nothing clipped.

Anyway, I do the impossible, decouple the orange tank arm, dock the tug with it, deorbit and land safely the Kerbals in the 'arm' delivery vehicle (mostly there for the SAS torque), and dock the transferred arm to the station.

Issue #2 - Nothing lines up correctly. The orange 'arm's' light towers are not at 90 degrees like they were in the VAB, and the tug did not connect to the 'arm' in the rotation it did in the VAB. With only vertical rotation in the VAB, why do the connections via docks in space not line up the same way?

Issue #3 - after connecting the orange 'arm', I left the tug connected to it, in order to place the other 3 arms coming later. Returning to the space center, there is no longer any station piece as a flight, only the tug. I cannot select the station core pod (T-Can) for targetting, and hence cannot change it's name/etc. It's as if the station decided the tug was the main part, and not the initial pod. I'm guessing this is a bug; both the tug and the station should be target-able.

So, what could I have done differently? Could I have constructed things differently to avoid these issues?