For this tutorial I will be using Adobe Photoshop 7. The way I do this will work in PaintShop Pro also, but with one step that is different. I will explain that step for PSP users once we get there.
Let's start with Body.tga
Open body.tga in Photoshop, and open the Channels tab of the box in the bottom right corner (by default). Click the "new channel" button.
Now go back to the Layers tab and create a New Layer. What I like to do is draw out my alpha channel in layers and then copy it over to the actual channel afterwards. PSP users can create a new layer as well by opening the layers toolbar and playing around.
Now before doing anything else save the file as a PSD, so that you can save your work in layers.
I'd recommend having the model open in Zmod again, and select all the faces which use the "body_ref" material (use the Select by Material command to make it easier). Now go to Surfaces-->Uv Mapping-->Assign UV. Make one of the viewports "uv mapper" and now we can see what parts of the car are mapped where. This makes it easier to know what we're doing to the texture. For your convencience I have made a picture that tells what parts of the texture do what.
(click for full size)
Now that we know where things are, we can start making the alpha channel. The way most of us do shaders, white alpha = 100% reflection, black alpha = 0% reflection, and then there's varying levels in between.
Citroen badge
This looks like chrome in the photos I found, so a high alpha value will be used. I think 240/240/240 (R/G/B) will be good.
Car paint
For my 456gt I used 64/64/64, Deyan's Murcielago uses values ranging from 150/150/150 (sides) to 225/225/225 (on the top parts). To be honest they don't look much different in reflectivity in-game. Basically you can choose a value that you think will look nice. If the car turns out too reflective in-game, then reduce the value, and vice versa. Since rally cars are just as reflective as normal cars, I'm going to use a value of 120/120/120 and we'll adjust later if needed.
Roof Scoop & little things on the roof
These are just as reflective as the rest of the painted objects, so I'll use the same value.
Front lights & rear lights
Again, I'll use the same value since they're about the same reflectivity. Feel free to do something else if you have better reference pics.
Rear wing
Finally something less reflective, so I'll use a value around 40/40/40.
Making the Basic alpha levels
On that new layer we created earlier, make a selection over the silver box the Citroen badge is on, and fill that with 240/240/240. Then select the sections that will use the car paint's reflectivity, and then fill that selection with 120/120/120. Now select the area of the rear wing texture and paint that 40/40/40. Make sure this is going on the new layer, not the base texture. You should end up with something like this:
NEXT WE ADD DETAIL