Regular counters don't work in other files such as EDCT. If you want to communicate information between CS and any other file, you must use event counters with I_EventCounter (or event_counter in EDB).
I have always used event counters for communicating with other files, in light of Gigantus' comment above, I figured this was only necessary for EDB and I was just doing it as a convention/preference for the other files. No, turns out it is absolutely necessary. I said before that all the conditions that work in CS also work in EDCT and other trigger files, and this may still be true, but those files cannot 'read' regular counters, only event counters. A Google search for the text of your log error
confirms this. When you get a weird error like that, it's usually a good idea to google it with some other key words like "twcenter", "medieval 2" (as TWC's in house search bar is totally useless).
You haven't provided enough information on the "too many cities" crash to even speculate on. Usually when factions die "unexpectedly" it's because all of their family members died - which can sometimes happen even if the faction has tons of settlements.
Here's a likely candidate for an accompanying crash that seems to afflict most mods.
The menu crash is
well known. It's a memory leak related to loading UI elements in the menu. You can induce it regardless of how many elements you have (i.e. how many faction icons). My guess is that a single button in the menu would be enough to cause this crash if you click it furiously enough for a long enough period of time. If you have close to 31 factions and tons of custom battle maps, it will crash immediately switching between those menus and the solution is to use a single image for all of your generic custom battle maps.