b) If I leave the rewrite rules then set $wgArticlePath = "$wgScript?title=$1"; then URL's of the format (http://wiki.themixingbowl.org/w/index.php?title=Special:Userlogin&return...) work fine again.
This seems odd to me... as far as I know, $wgArticlePath is only used when automatically generating links, it shouldn't have any affect when going directly to a URL. You should probably have it set to "/wiki/$1" rather than just "/$1", though, otherwise you'll have problems with articles called things like "w/" or "robots.txt".