At some moment, I tryed to make 60-70 mm (2 1/2 - 3 inch) high each floor for easy of meneuvering miniatures inside, but found it too complicated, because there are some players that are VERY strict about distances (for climbs or falls) so, for easy of gameplay, I now stick with 2 inch floors too.
Actually, the "Mordheim boxed set" card buidings, has 55mm tall first floors, while every floor above groud level are 50mm.
A good rule, as more often than not, action happens on ground level, and that extra 5 mm will hardly get objected and is really useful.
About wall lenght, some people likes to make massive buildings.
Imo, 100-120 mm (4-5 inches) is about right for average buildings.
Also, I try not to make buidings with more than 3 levels, as they rarely got used in my games (maybe is just us, your group can be multilevel, aerial combats fans).
The most important rule, however, is that you don't have to be a master builder to try your hand at it.
Everybody learns by making mistakes, and you'll learn a lot once you try.
And, as this is Mordheim, and the buildings ARE SUPPOSED to be destroyed, you can claim that any misfit was made on purpose.
Look around here for inspiring pics, but don't be too ambitious for your first project.
Hope that helps.