Gerasym & Cossacks, I'm sorry I haven't been much of a help with these issues, thing is, I never made a scenario this way.
The information on this site about this, i got from the Cossacks Tech Depot Site which was run by the Cossacks Engineer Brigade.
Unfortunately this great site has gone offline this summer.
However, if you want additional information or help, i ran a search with the Web Archiver to trace the site back and see if there was anything else that might be helpfull.
Have a go at this tool: http://www.archive.org/web/web.php Web Archive
and run a search on http://www.geocities.com/cossackstechdepot/, or the direct link to that would be: http://web.archive.org/web....ttp
I looked for the emails of the Engineering Brigade:
MarionVonGhent, email@example.com ( last I heard of her, she was moving to China , so dont think you will get in contact with her.)
General Monty, firstname.lastname@example.org
Mr.Nice, email@example.com (the one you should get in contact with, he made tools for modding etc...probably the one with the biggest knowledge.)
Try contacting them, see if any email is still active,....
Additionnally, you may want to get in touch with the [HAWKS], they used to make maps for The Art Of War, but then they switched to the American Conquest series. They are great map makers, and maybe a couple people there might be able to help you with the problems you are encountering.
Especially [HWK]Garnier knows a thing or 2 about making scenario's this way.
They also have an updated ( fixed) scenario editor for one of their mods ( HEW~Hawks European Warfare, by Gexozoid). Inquire on that perhaps aswell, since i noticed you tried to fix the scenario editor yourself. Not sure if its compatible with Cossacks though.