Grimber:
Applying the FX to the level would not be all that hard. However, I think that a fast reply is not going to help you. There are a few things to consider that will help with the performance when applying an FX to level geometry.
If I can find some time I will work something out. Right now there are things on my list to followup on and very little time.

indiGLOW:
For the dynamic lighting you would need to incorporate the dynamic light positions into the shader code. Some other things that I have never worked out was successfully getting the level light and ambient colors into the diffuse. I had to resort to hard coding those typse of values in.
For static lights you would also need to incorporate something into the shader code. I cannot find the code I had where I had made progress on these particular things. I believe it to be nixed from my computer. Which is very, very bad.

The Hi-lights/specular you refer to will have to be coded into the shader. A gloss/specular or darkmapping type thing is not in the code I put here. This code had been abandoned.

By multi-passing you can combine some things. With FFP it is easier to use the framebuffer continually down the passes. With the vetex/pixel shaders it is not always the case unless you can pass the result from the previous pass into a texture. Also I have noticed that alot of codes will render_mesh, render_technique, render_mesh, render_technique. And so on, blending as they go.

I think that the other issues you wrote about are based on the normals. So depending on the orinetation to the light source/model normals you might see some difference in the bumpmapping. I can't make out from your screenshot so well.

There tends to be the need to tweak things per model and particular situation, which is no big deal if you know what you're tweaking and what you want to accomplish. But it can be tedious at best if you do not know.