Making a wall seamless across different heights?

I can help you out here. first your walls will look ok in game, the templates you are using are a different size that's all and its shows in S4S. 

I use the Abour walls as a template for all my walls. The texture sizes are; Small- 256 x 768. Med 256 x 1024 Large 256 x 1280. The bump and spec textures are the same size too.

The medium wall is a bugger, I'm sure the mesh was just dragged upward and then not properly unwrapped so in some walls it will always appear a little stretched in s4s and the bottom moulding will not line up with the other two sizes, but it makes no difference in game. A perfect example is any x4 walls or walls that have a single texture across 4 tiles instead of 1. (eg Pretty in Plaster) 

I have a folder with these walls as blanks so I use them as a template for all the walls I make, it saves resizing every time I want to make new walls. I hope this helps