...I'm not completely stupid in not figuring out the issue myself.
Yeah don't worry about that, this isn't exactly regular modding stuff.
Do you have any idea how this mess could have happened? Maybe had the San Fran map open in the Mapper before going to your map, and also doing some play testing (F8 mode) as the player script was one of those embedded scripts?
Anyway, here's a small step by step to fix the map:
Set "save_text_maps=1" in mapper2.cfg.
Backup your map!
Start Mapper and load your map. Now you want to create an almost empty version of your map, so from the drop down menu "clear map level" on all levels and "delete ALL spatial scripts" (not sure if it deletes all or if you have to do it on each level).
Save the map and exit. Go to your map folder and open the text version of the map.
Scroll down to the script section (scr_num: ) and you should see 8 scripts there. These are the ones you want to remove later so keep that file open or move it to another folder so it don't get overwritten.
Now copy your backup of the map back in the map folder and start the Mapper. Load your map and just save it again and exit.
Open the text file map you just created and search for "scr_num: 10" and change it to "scr_num: 2". Then remove 8 of the scripts (the ones from your first text map). Basically, you only want to keep scripts with scr_script_idx: 1200 and 1201 in that part of the script section.
Save and go back into the Mapper to recreate the map. "Open from text" is broken and will crash the Mapper, so you will have to use "rebuild all maps" instead. Make sure your map is the only map text file in your folder so you don't create others unnecessarily.
Now that the map is back to normal again you'll have to fix a few things, as saving a map into a text file doesn't save everything correctly. It breaks the green exit grids and ladder data, and those will have to be reset. Inventory items also gets screwed (the amounts of items and their weight) so they will need to be replaced in containers and on critters too.
If you are good with a hex editor you can of course skip the whole map to text thing and remove it directly.
I did it once and well, lets just say that I'll never try that again...
Hope that helps.
Or you can just skip the above and
take the map I fixed while writing this stuff. I think everything is good but you better check it just in case.