A bit late, but in terms of getting out of your situation the only two shortages you might have needed to fix were the Rare Crystals and Energy Credits. The Rare Crystals would have probably bumped up the minerals & alloys production into the positive, and if not, then energy shortage would have bumped minerals into the positive. That would have fixed the mineral shortage which subsequently could have possibly have fixed the consumer goods shortage if you lowered the living standards down.
Two other items which affect consumer goods production are your trade policy (switch from credits to credits + consumer goods), though it would mean selling more onto the market and having a civilian economy policy for +15% consumer goods manufacture. Changing to strict rationing might help with food if you haven't changed that as well.
You would only have needed to fix the shortages during the monthly rollover (& not permanently to start), which would have been as simple as selling the other strategic resources and leaving at least 4 crystals and 128 credits in the bank. I would have also recommended buying enough food and consumer goods to end those shortages if they persisted and seen where your production ends up.
You would likely need to keep selling resources and buying the 4 crystals & leaving 128 credits leftover/month until you had positive crystal, energy credit, and consumer goods income. Turning off research buildings would resolve consumer goods temporarily, while turning off upgraded culture/unity buildings would help with both consumer goods & rare crystals. Unfortunately rare crystals seem to be the most in demand strategic because it's used with consumer goods manufacturies, advanced housing, advanced trade and culture/unity buildings, which means most are a necessary expense to fix the economy.
Upkeep of civilian ships is still 0.75 energy/month as far as I know so it would have helped disbanding most of them, but the real issue would have been re-balancing the crystal & consumer goods production permanently, and selling excess production for energy credits.