I used the Morrowind Code Patch to make my map bigger (to allow space for Tamriel Rebuilt). But when I want to revert back to standard map size it doesn't work. The new smaller map stays on top of the old one. How can I fix this?

You could just take the old executable and re-apply whichever tweaks you want to keep...

I am not sure what you mean.

Basically when I am now at Azura's coast somewhere it shows me as being a whole lot farther to the West.

I believe you are supposed to use wyre mash on your save.

I tried that and now my vanilla-sized map is on top of the smaller map

And the map is split in these big squares.

Your best chance to get some help with this is to post your issue in the http://www.gamesas.com/topic/1244500-repairing-the-cogs-of-morrowind-27/ thread.

Take the backup of Morrowind.exe from before you made any changes with the Morrowind Code Patch, and that has the normal sized map. Now just re-apply any patches you want to keep with MCP.

Doesn't work either. It seems to me that the issue is with the savegame, because even if I run it in Vanilla Morrowind it stays the same.

Luckily, I made a backup of it after making this thread so this issue remains the same as in my first post.

Thanks, I'll try that.