Making mistakes is part of the fun
The TOS captain can only be human, vulcan, andorian, and...tellerite?...even if you unlock other races like catian-totally-not-Kzinti, liberated borg, or talaxian chef. Try creating a TOS to see the races.
Tractors are nasty at low levels. The ways to escape are Evasive Maneuvers (not sure what level you get it at) or more reliably teaching your science bridge officer the Polarize Hull skill.
Mortars are handy on the ground if you can set them up before entering combat.
Very few episodes use static or the flashlight, and only one raid I can think of (Romulan station).
> I now have 2 borg packs I can’t currently use and no Zeni. Borg engineer I am using is female and called 6 of 9… Nice.
Are the packs listed as bound to character, bound to account, or neither? If not bound, you can sell them on the exchange for a small mountain of Energy Credits to use to buy other things. If bound to character, support might refund your zen since you can't use them.
> I can’t tell if this poor UI or dumb thing #4. Clicked on the transwarp button on the top mission. Do mission with a strong sense I’m missing some context in regards to the story. Do next mission. Oh heyyyy, this is most the stuff they were referring to from the previous mission. Why is there a ‘to be continued’? Click around some menus and find I did missions 4 & 3 of the Terran Gambit…
It's a really dumb UI decision. You get offered hails from people offering you missions from a bunch of different story arcs at once, instead of just from the first arc. The mission journal shows you all of the different story arcs in order so you can play them in that correct order if you want.
The only out-of-order episodes you might want to do are the ones for the current event, but you can do the raids / Task Force Operations instead if your level is high enough.