Which modifiers? Or maybe, where in the DLL?
Modifiers.py. As a guess, Distance to Capital Maintenance and Number of Cities Maintenance. Preferably lowered per-civ based on by what how much their intended distance and city number has increased.
As there are already issues with research and commerce in general, it may be necessary to increase the Inflation Rate to keep their economic growth in line with DOC.
I recommend against raising or lowering the Research Cost modifier, as any issue that requires such action is indicative of a greater commerce issue.
Lowering Unit Upkeep is probably necessary considering how many more units will be needed to protect nations and wage war.
I don't know enough about how Civic Upkeep is calculated to really be of any use in advising what to do with it.
None of the production cost modifiers should be necessary, as afaik you haven't made any changes to the potential production output of cities per nation. This would be things like adding production resources in production poor regions or adding buildings or building effects that increase production. If so you may have to reexamine them and decide if they should be left as is or not.
Growth Threshold is similar to production but with food, health, happiness, and growth speed.
Great Person threshold etc etc but with GPP and Specialist Slots.
Health etc etc but with Health
Culture etc etc but with Culture
TL;DR Change the Distance and Number of Cities Maintenance proportional to how much the intended max distance of cities and intended average number of cities have increased. Increase or Decrease Inflation Rate to fix issues with rampant economies. Don't change Research Cost unless you must, as a requirement to do so is generally be indicative of an issue with the overall economy compared to DOC. Lower Unit Upkeep if nations should be fielding more Units on average. Don't touch any other modifiers unless you've made changes to the prospective output of that resource in a particular civ.