Why should the Shek hoard every city after you take down the Holy Nation? Wage war against the Shek, side with Moll to retake the former Holy territory for the Flotsam and help them become a fully fledged nation, with regular troops, shops, farms etc. 

Become allied with Moll and start dismantling the Holy Nation as normal, and once you're done set your sight on the Shek: Stack and Bad Teeth have new, powerful leaders. Defeat them while allied with the Flotsam and the Ninjas will take the cities over. You can even help Moll take over The Hub, but it's gonna be harder. Speak with Moll at Blister Hill after each step to know more (or read the spoilers below). 

This is the main mod, I recommend to try this one first because it's more complete and with more flavour. It requires Reactive World, New Weapon Dissemination Mod, More Plates and my Holy Nation and Shek new Weapon Grades with Horned Devils. All mods are linked in the Rquirements section. 

There are other versions with less requirements below.

In the optional files are a version without NWDM mod and one without the Horned Devils and now a patch to only removed the Horned Devils while keeping everything else. Only use one file, be it the main file or one of the two optional files, ONLY ONE. Even with the optional files you still need the other required mods, they only cut out one mod each. The only exception is the patch to remove the Horned Devils bandits, that one goes together with the main file, below in load order.