Atram,
I've looked at your savegame.
The reason for your debt is due to a higher monthly expenditure as compared to your income. Once your treasury drops below -500bcs, the economy goes into shutdown mode. This means that all your resources are channelled into cash to restore your treasury above that level. That is why you see yourself getting a big surplus in your accounts. Once the empire treasury returns to >-500bcs, you need to change your spending slider to make sure that your net change in treasury is positive on a monthly basis. Else you will continue slip into a cycle of going into debt, shutdown & restore.
Some tips on how to improve your overall game:
1) Build more social improvements that help your morale, industry, research and economy. Very useful social improvements include all those with zero maintenance, entertainment network, fusion power plant, stock market, research lab, anti-matter power plants, teleporters, economic exchange, etc. You should use a governor with a queue list to reduce micromanagement.
2) Scrap (go to planet details, click on the improvement on the left list and select cancel project) projects that are no longer useful. You have news networks, planetary defenses and cultural exchange centres deep in your own territory. These aren't going to be useful but they sap your cash every month.
3) Build constructors and mine those resources. Since you currently have problems keeping up your morale (in the fifties range with tax rate only at the thirties), it would be a good idea to go for morale resources (don't forget to build those morale improvements as well). Other resources are also very useful.
4) Reduce your huge military. Your current military rating is 304 but if you move all those ships that you have sitting next to your systems into orbit (being in orbit increases the ship attack) your military rating would shoot up further. You can scrap (no money back) or better yet sell or trade all those scores of defenders, starfighters, battle cruisers to the AIs. Your numerous frigates and battle hammers are sufficient to deal with the remaining AIs. Ships cost maintenance, so spending 1/3 of your income on maintenance means much less for social improvements and research.
That's all for now. Let us know if you have more questions. Have fun.
~SDC~