I'll second Themken's remark.

You will probably want to start a new save. The goods news is that, with all you've learned about the game, as long as you're willing to pay the iron price for your ships, then you can get back up and running again quickly. That said, transferring marines one at a time over and over again is incredibly frustrating, so waiting for 3.0 and mass crew transfer might not be a bad idea.

But in case anyone wants some ideas for how to jumpstart a new save:

* get yourself a 4star pilot and put them on a medium Teladi miner. Set it to mine Nvidium only, and to automine with an anchor space where the range 4 is within all 4 trading stations that buy Nvidium. It'll mint you about a million credits an hour indefinitely. FYI, the demand won't regenerate fast enough to keep up with the supply that more than one miner would provide.

* bail a Minotaur Raider. Load it up with bolt weapons. Put 12-15 marines on it.

* buy a Callisto Vanguard at the ALI wharf. Minimum preset, switch to PAR Travel Engine Mk1. This should set you back ~115k credits. You can sell it for ~75k credits. So for 40k credits, you can buy 2-4star pilots that you can dock at your acquisitions.

* go to Nopelios VI or Pontifex's Claim and wait for a Selene/Helios Vanguard with at least Mk2 thrusters. (Mk3 is ideal, but rare on freighters.) Scan it. Make sure that your marines have a chance. If not, either keep hunting or, if you actually find a Mk3, pew pew it until enough crew bails. Capture it.

* reequip it as you see fit, and the put drag and rotation thrust mods on it. (Rotation thrust only for your in-sector assault ship. Use forward thrust mods for autotraders.) Load it up with marines.

* use the Zap Brannigan approach of sending wave after wave of your (newly recruited) men to capture new freighters. Until 3.0 comes out with mass transfers, it's too annoying to move troops around, so just use 30ish rookies each time.

You can find miners in Nope II, and obviously once you have your Assault Ship, you can easily claim SCA Plunderers. Just continue to engage in wanton piracy of capital ships until your new empire is on its feet. As long as you don't destroy anymore modules than you absolute need to (turrets), your traders will be able to repair the rep damage.

PS: I see all the discussions on Steam about whether Medium Freighers or Large Freighters provide better ROI. Well, as long as you pay the iron price, the answer is clearly Large Freighters, since they only cost you ~150k worth of marines.