I think you'd have to edit the current size of each city if you want to give them a higher population. The way they are now wouldnt fit that many people, since Bethesda designed them as such. It really is a shame that they are so small. I would have loved to see Assassin's Creed size cities with TES lore behind them. If you could pull it off though it'd be one of the better mods for sure.
Try disabling Vals Crafting mod if you have it. I was having the same problems, no menu, no music, only smoke and dragon logo. Once I disabled the mod it worked!