Uhhh how these work is you have 3 layers:
1st: You have the background to the timer frame image\Sinimage\skill\keep\GA_.tga
2nd: On top of the background you have the timer.
3rd: Then on top of everything you have the force orbs image.
-->
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So as the middle timer layer increases it covers up the bottom background layer, then only the background and timer and appear through the transparent bar in the top layer.
In regard to patching TGA's one at a time...
You what?
Use bobsobols pt file patcher.
http://forum.ragezone.com/f399/pt-file-patcher-684994/
Make a copy of your pristontale folder. <- Because it WILL break the game!
Drag the copied pristontale folder directly onto the file patcher exe.
It will then auto convert all bmps and tgas to readable format.
Then to make life even more easier, you want a tool called sagethumbs:
You must be registered to see links
This will generate thumbnails for all sorts of weird and wonderfull image/video formats that windows can't generate on its own, allowing you to view thumbnails of the TGA files, so you don't need to open one at a time.
Yeah, sorry mate.
The timer bar colour is hard coded in the game exe.
If you want to change it, you will have to track it down somehow and change it, assembly or hex or actual code, if you are using that, who knows.