I also had a nice chuck of time where my gold income was showing as -40 to -50ish a turn for a while, but my bank was actually increasing

And no, I wasn't pillaging for gold or taking cities during this time, nor did any of my units have the "get gold when you win battles" ability.
I don't know that I'm going to describe what was happening to you, but this is the most likely culprit. If one of your cities has an extraordinary amount of production, the hammer overflow from that city's production turns into gold. Imagine a city with 100 hammers per turn building a 30 hammer military unit.
Turn 1: 100 hammers goes into unit. Unit needs 30 hammers. A max of 30 hammers can go to hammer overflow for next turn because Civ won't overflow more hammers than a unit/building actually costs.
You have 40 hammers of production that can't go into the overflow, so Civ/FfH turns that into 40 gold.
Turn 2: 130 hammers go into the unit because you have 30 hammers of overflow. The unit consumes 30 of those hammers, so 100 hammers are available for overflow. 30 goes to hammer overflow for next turn and 70 goes to gold.
rinse and repeat.
Now, build the Heroic Epic in that city and watch the fun explode.
Sidar, Clan of Embers and Kazad can have some real fun with this trick. If they adopt Runes of Killmorph, they won't get nearly as much gold, but they can build the little mini-engineer dudes so that they can turn those Heroic Epic hammers into buildings/wonders in other cities and not worry about deleting all of those "surplus" units.
This trick is often abused in regular civ with cheap buildings that get production bonuses. Creative Libraries or especially Walls for a Protective Civ with Stone. Put a little production into the Walls and then

them to completion on the same turn that you chopped down a couple of trees and watch in amazement as several hundred gold drops into your treasury overnight.