Well, let's walk through this using the built in ATSF SS Baggage Car,<kuid:-1:100159>
That one is a build 2.9, so the simplest way to fix all the missing obsolete whatever tags is to open it in content creator, find the tags it's complaining about and click the X button to delete each one if it doesn't do it automatically. For this one the obsolete tag was deleted and the required category-class ZX was added automatically so all I had to do was save and exit content creator.
First two are fixed automatically by opening in content creator and saving, the missing texture.txt error is what you fix with Images2TGA - it's unaware that built in content compiles whatever.texture.txt and whatever.tga into a single whatever.texture file, so it can't find the actual filename it's looking for and sulks. For non-built in content the compiled whatever.texture files are not used, so once Images2TGA decompiles it into the whatever.texture.txt and whatever.tga files, commiting automatically deletes the original whatever.texture file.
If it's set up correctly, right click and select Open With, choose Images2TGA.bat, and it should do the rest automagically. Not working for me right now, possibly because I'm running this copy of TS12 from the F drive. So do it manually, open for edit in explorer, select each whatever.texture file, open with Images2TGA;
Then Save As, and it will create the whatever.texture.txt and whatever.tga file. Do that for all of them including the shadow.texture if the automatic bat fails. Should end up with something like this in the explorer window;
Provided you don't have pretty pictures with file extensions hidden, if you're gonna hack files you really should change that;
http://www.trainsim.com/vbts/showthread.php?304396-Windows-Explorer-for-dummies
Because it's a whole lot easier to tell the difference between whatever.texture and whatever.texture.txt if you're looking at actual filenames with the extension not hidden.
After that edit, commit, check for errors.
