I use 2 inches for floor height. It is a little squat in terms of gaming, but 3 inches is almost three times as tall as a human at 28mm. It would be like if all of us lived in buildings with 15 foot ceilings.
This height is a little short for larger races, but when I make a ruined building, every higher floor has a slightly smaller or offset surface area than the floor below it. This allows one easier access to the floors, but it also gives a little wiggle room for models that are too tall for a floor or are posed in a very dynamic manner with spears or two-handed weapons.
I like my Mordheim table to look like it is filled with sagging, ruined houses huddled together on winding streets. The shorter floors help to create a visual sense that the buildings are cramped and crowded. Now, I also like to build lots of balconies and other areas that aren't covered by a ceiling or roof. Again, this helps to create areas where larger models can be placed in elevated positions.
If you are trying to make your table dynamic, I suggest using different levels of elevation, both with structures like houses and with variously-sized platforms on which additional terrain can be placed. These platforms can be used to simulate canals, sewers, different street levels, etc. (http://mordheim.ashtonsanders.com/2008/07/09/gold-mordheim-terrain/) this is a good example of what I'm talking about.
I also suggest making stairs, ladders, and bridges that aren't connected to another piece of terrain. That way you can set up your table however you like and your terrain pieces aren't railroaded into a certain configuration.
Typically what my group does is set up buildings how we want them to be and then we evenly distribute ladders, stairs, ropes, etc. and take turns placing them around the table. This way both players get a say in which buildings are easy to access from which point.
In terms of building footprint, What I've been doing is constructing my ruined buildings on small bases that are just about a half inch larger than the perimeter of the lowest level. For the lowest level, I use all kinds of sizes, but the most common rage between 5 and 8 inches or thereabouts. Then I tier the higher levels. This is of course a very Mordheimish aesthetic, but what it also does is allow you to jam two adjacent buildings together (so you can run across rooftops, jump between windows, etc.) while still leaving room at the "street" level for models to move around (because the buildings wider upper stories are what's touching).
On a final note, I suggest putting windows in your buildings, but leaving some walls without windows and putting the windows in some houses farther apart. The reason is that this helps to create areas that block LOS, which I think is important to help balance the relative strength of primarily ranged warbands. You are probably used to doing the same thing with your 40K terrain. The reason I mention it is because folks can sometimes get window happy when making houses. Oftentimes in a Mordheim game, most of the terrain on the table consists of houses, and if every one has windows all around on every floor, you might find yourself wishing you had a hill to hide behind.