Effectively i discussed already the issue with your problems in the
help section.
viewtopic.php?f=5&t=1045My proposal is to implement management of rectangular sizes via sgf tag SZ[a:b] (which is part of the sgf standard, i don't invent it) instead of SZ[n] to support irregular boards.
Else you have to give up the idea and fill space with stones, problems will look heavier but at least less confusing.