For the frame colour I'd recommend using Hue/Saturation, Colorise and use the sliders to find your desired colour. On the colour layer you can paint in whatever colour you want. Copy and paste an existing frame, shadow and colour into the new slot(s). If you're making more, extend the width of the image by 25 pixels per additional frame. If you're making the "highlighted" strip, make sure you selection layer is active and copy+paste the "Selected Alpha" to the alpha channel. If you're making the greyscale strip, as above and make sure the "Greyscale" layer is active and the blend mode is still "Color". If you're making the standard strip copy and paste the "Standard Alpha" to the alpha channel. You can't save the religious icons in TGA format, for example.)
(Though do note that with CK2 TGA and DDS are not always interchangeable. If saving 1k or so on file size is really important, use compressed TGA instead it has loss-less compression which works reasonably well on icon type images and still reduces the file size. I suggest reading the Wikipedia page on the DDS format for some quick tips on which option is suitable for your image, but in the case of very small small images it's generally best to avoid compression altogether.
Opened Hroppa's XCF version of the template.Without knowing exactly what process you used, it's hard to say where it went wrong, but here's how I went about it when I tested: I just tested Hroppa's GIMP versions and they seem fine.