Nicely done again Capt'n!
One "trick", one hint and one response:
1 - When storming those UFOs, I found it very convenient to have a gal with a flamethrower cook all the enemies inside. Flames don't break stuff, so you don't have to worry about loot like you would with explosives, and the AI doesn't like standing in it, so some tend to come out, but in a more scattered way (since they need to walk in the fire to get out), which means it is a bit safer to approach. If they don't come out, apply more fire
Eventually, because of the combination of smoke and burns and running around/out, the enemy will be weak enough you can storm what's left.
2 - Many guns are not worth selling for money. The runts aren't great at building precision parts to make fancy cool guns, but eventually they will be able to scavenge parts from multiple guns to build a fancier version. It's worth holding on to "random guns" (anything you can't buy on the black market) even if you don't think you will use them in battle. Also, sometimes the brainerz discover new things that old guns can shoot.
3 - You asked for advice on what to do next. My take on it is: Build an extra workshop and a living quarter to house runts and also more gals. We need many gals to ensure the Bonny is fully crewed with the kind of injury rate we have. And fully man the existing workshop if it's not done yet.
Piratez is a money game. You pay a lot for maintenance and you need to invest to build, which in turn increases your maintenance. Looting is great for getting initial investment money, but booze-making is central to making a sustainable enterprise. Some months can by too hot (only shipping you don't want to take on) or completely dry (shipping in regions you can't see), you need to be able to balance the budget any ways. If you build up your booze adventure enough, it can be a "runaway money train", since more production = more money = more investment = even more production = even more money and so on.
Of course, some of that more money should be invested elsewhere once the budget looks good: moar brainerz! And maybe a pigeon hideout to remote scouting, but both are longer term. Getting the money train started and Bonny crewed are more important.