In recent, I have come across a difficultly. I can not change the lighting within the Truth and Reconciliation shuttle bay, or the control room. I can't locate the tags or the bitmaps needed to do so, and am wondering what I can do about this.

What I'm attempting to do is change the lighting to a dark red, and make the control room 95% pitch black, with the exception of those dim red lights.

That, and I also wonder how I can create an atmospheric effect that's similar to what was seen in the Halo 2 level High Charity and when The Flood took over the whole station (i.e. all the Flood spores and gases that almost obscured everything visible).

Anyone have advice or help?

If you want to change the lighting you will need to rerun lightmaps.
You need to open the different shaders for T&R and find the ones that emit light. Look at the top of the shaders and edit the radiosity properties section. Lower "power" to a smaller number and change "color of emitted light" to whatever you want. If you don't want that shader to emit any light then set power to 0 or color to black. You may also want to change the illumination in the shader_enviroment tags to red (for those that have illumination). Some of the bitmaps you may also need to recolor to get your red as most light bitmaps are white/blue/purple.

For example: you will want to change the shader levels\a50\shaders\covenant bright light white.shader_transparent_chicago and lower the power way down and change your color to dark red.
A bitmap that you may want to recolor to fit your environment would be levels\a50\bitmaps\covenant lights strip.bitmap

To get the atmospheric effect you can change the sky tags for a50 and add an "indoor fog color" and change the density.
To get the spores you need to add a weather particle_system tag with the spores in it. To add this to the bsp you will need to open your bsp in an unlocked Guerilla (OS or kornman00v2) and find the "Weather Pallet" section and add your tag here and name it and add some wind if you want. Then go up in the bsp tag to "Clusters" and change weather from NONE to your weather name. Do this for all the clusters. You can also do this in Sapien except that you will have to go into every cluster to change the weather so you might accidentally skip one.

10/10 post.

How would I rerun the lightmaps?

In open up tool in CMD and type "tool lightmaps levels\yourlevel\scenario_name name_of_bsp 0 0.9"

Example:
tool lightmaps levels\a50\a50 a50_control 0 0.9

a50_control is the .scenario_structure_bsp name for the control room part of the map.
a50 is the name of the .scenario file for T&R.

The first 0 controls the qualtiy: 0 for low and fast, 1 for high and slow.
The second number controls where to stop the countdown for calculating lightmaps. The closer to 1 the faster your lightmaps but the lower quality. The closer to 0.000001 the higher the quality but longer time.
Also, when you first test lightmaps, use 0 for quality and a second number such as 0.9 or so.

Make sure you make a backup of the original a50 bsp tags and lightmap bitmaps for those bsps that you are going to run lightmaps on.

After you get your shaders set up and you test your lightmaps on low quality, you will want to run high quality lightmaps (use 1 and 0.0001 or smaller). However, this will take a LONG time but will produce better looking lightmaps so only do this when you think you are finished.