I think (keyword there) that you should do the vgares tool again, but set it to vertical and have it generate new ini files. then launch each game and using the TAB menu, rotate each game until it's in the right position. IIRC, that's what I did on my machine (cocktail galaga, so it should be identical to yours monitor wise.)
Just plug in a keyboard while you're doing this-as I said, it's a one time job, so don't bother mapping a button to it.
There are a few other video options available through that menu, but you shouldn't have to mess with any custom resolutions. It was at least 9 months since I last messed with my video options, so my memory is fuzzy. I have an arcadeVGA running into a standard res WG 19" monitor too, and after rotating everything into place, I don't recall having many video problems.