In Jonathan Swift's "A Modest Proposal", he elaborates on an unfavorable balance of trade with England. To what is he referring?

The unfavorable balance has to do with England's use of Ireland's resources to the detriment of the Irish people.  Food, crops were exported to England while the poor Irish people were left to starve. 

In "A Modest Proposal," Swift is discussing the unfavorable use by England of Ireland's resources.  England, the dominant power, exported Ireland's crops for their own consumption, leaving the Irish, literally to starve. Swift's satire regarding the consumption needs of England, seemingly like a ravenous beast, suggests that the English begin to utilize the children of the poor Irish as their new food source.

What he is talking about, of course, is the fact that England is robbing the Irish of their very survival by removing their food crops, and the disparity between rich and poor is growing larger by the each passing day.

Swift is really making a political statement about the misuse of resources, the tyranny of the English against the Irish and the lack of proper governing provided by Irish politicians. He is also disappointed by the lack of fight against this inequality from the Irish people.