[nocalora29]

I was wondering, is this how the Mothership is supposed to look ( just so that I know I have installed it right, my Video settings are little lower so it does not look great as it should be )?

Well, I guess it looks kinda blurry because of the graphical settings, but it should look like that, but heres be aware that this Ship shouldn't be used as of yet, since it has many missing Collisionspheres, because of that only few ships will be able to hit it, and the GUI-Slots aren't Ready for this ship as of yet.

This is the image (in a Trade station) of a Shield booster for Mothership

Doesn't seem too gamebreaking, Seemingly only an texture file is missing.

There was a message about a successful switch of ships in Gredos system when I got a mission to transfer goods to Copernicus station in a new ship.

I recommend replaying to the gredos part with the original tug ship the game gives you, since the MSSWitchBlock seems to mess something up there, until its fixed I recommend playing the Vanilla ships until you get to a part where you have much time before a new Mothership change by the Story.
btw: Did you had the Freedomkiller Blocker turned on?, if not try it again with it, It blocks many of Star Wolves Self-proclaimed "Freedom-Killers" which simply blow up the Ship.

Thanks for this very useful Bugreport mate, and praise the logfile, it also told me about other stuff which makes errors (Including a thing which massacres the performance)

I will have the fix ready very soon, but the thing with the MSSwitchBlock is kinda tricky, we'll see about that.