raystuttgart
Civ4Col Modder
Is there a tutorial out there that fully explains what is going on in the tga?
Not to my knowledge, sorry.

Sadly (for community) a lot of technical discussions between modders to solve certain problems have taken place in private team forums or private messages.
Others are spread over many many threads and really hard to follow. Some of these threads are in other languages (e.g. German).
My best tip for you is to set up "Extra-Large-GameFonts" really early in your project.
(As an example check the Gamefonts of RaR. But it is pretty much up to you, how you want to create yours.)
By the way, the idea of such "Extra-Large-GameFonts" is not mine.
(It was used in Civ4 mods first and KJ_Jansson brought it to my attention.)
Leave space for many Yields, Specialbuildings, Missioning Crosses, ...
If you do that correctly, you will have almost no trouble with shifted icons anymore.
If you don't you will most likely have shifted icons almost every time you add something new in the GameFonts.
Otherwise it is a good idea to use a combination of these 3 Tools for working in the GameFonts:
Gimp2, DXTBmp, GameFontEditor
-------------
These GameFonts are the most stupid construct I have ever seen in Programming ...
Some references are resolved in Namespaces pointing to a certain position, some are direclty related to orders in Enums of the DLL, some are referenced by an XML tag and some ...
Almost every line fo the GameFonts obeys to a different logic.

So even not touching the GameFonts directly but simply inserting a new Yield in DLL and XML may shift the icons.
-------------
Edit:
Here is a discussion about Graphics and GameFonts in one of my old projects.
(At that point of time I started that project I had almost no idea about GameFonts at all. Without KJ_Jansson I would have been lost.)
I am not sure however, how much useful information can be found in that thread.