It's all about mounting the new icons on the background grid with unerring precision. I rebuilt these files about six times before I finally understood the right technique for doing it and had the cut and paste skills to pull it off. I, too, wasw on the verge of giving up a few times, ready to accept the minor anomalies that kept cropping up among my icons. But obsessive-compulsiveness won out and I found I could do it.
First off, I discovered that any minor (invisible to you) error in mounting the icons will throw the software out of whack and it will start assigning icons randomly. But then I discovered that if you have a problem like two icons sticking together, it doesn't mean that the error in mounting was committed while pasting in those partricular icons. The error could be somewhere else.
Now I didn't use photoshop so a lot of specific tiips I can provide won't be useful unless you change to Gimp. You can dl it free at
www.gimp.org. I did look at photoshop and I found (at a cursory glance) Gimp to be more precise and clearer at least as far as mounting stuff in the icon files goes.
One tip I can give is this (you may be doing it already):
1. Start with a fresh set of files
2. Save a fairly advanced game
3. Alter 1 set of four icons in the GameFont and GameFont_75 files. Save it in your mod folder.
4. Start your saved game. Check to see if a) the new icons appear and b) if any anomalies have appeared affecting other icons. If a) is no OR b) is yes, then...
5. You screwed up. Re-do those four icons. Re-load the saved game. Check again. Repeat this until you've got it right.
6. Now, very important: save the altered gamefont files before making any more changes.
7. Proceed to the next set of four icons. Repeat steps 3 and 4. If new problem appears, trash both files and start again from the altered files you saved, the ones that work.
8. When you've got your second set of icons functioning properly, save the files somewhere, and proceed to your third set of icons. Repeat as often as necessary.
This probably seems patronizing or something and I really don't mean to come off that way so please accept my apology if I do! But by applying this regimen strictly I was able to replace all the religion icons and holy city icons and have them run perfectly.
If you do switch to Gimp, let me know and I'll give you some specific technical pointers. Good luck!