Hi Will, for the multi-monitor issue #3, see this post here on an operating system setting that you can change which should then work better:
http://moi3d.com/forum/index.php?webtag=MOI&msg=6337.3

re: long startup time, I seem to remember there was at one point a problem with wineskin leaving old prefs files around or something like that, which once they accumulated to a certain level could then slow things down. I thought that didn't apply anymore to the version that MoI is currently using but maybe it does. Check if you have a huge number of files in ~/Library/Preferences like 2543243142241.wineskin.prefs.plist (with the same last part but different prefix numbers) and remove them.

re: multitouch not working - that's the first I've heard of this problem, right now I don't have any clue about that, probably will need some help tracking that down.

Thanks, - Michael