I don't think that there's a way to edit the city radii directly(sorry). However, you can change the way culture affects a city's borders. In Civ3Edit, under Rules/General Settings and in the Culture box, you can change the Level Multiplier and Border Factor of culture. This somehow changes the effects of a city's culture on its radius, though I'm not sure exactly how. I guess that Border Factor changes what happens to the city's radius when its Culture Bar thing is filled up, and the Level Multiplier changes how the number of points needed for the next level of the Culture Bar changes.
There certainly is a way to do the thing you mentioned with the mining and irrigation. In Civ3Edit, you can change the cost of tile improvements under Rules/Worker Jobs (in Turns to Complete), and you can change their effects on terrain in Rules/Terrain (under Terraform Bonuses).
Here's a tip on limiting city sizes, if that'll help you. First, go to Rules/General Settings in Civ3Edit. There, in the box labeled City Size Levels, you can change the number to the left of Town to higher than the default (6). What this means is that you can't get past however many citizens per city until you get an aqueduct in a city.
I hope these tips help. Try them out first with a test scenario to see what they do. I think the first one can solve your problem, but I'm not sure.