You may be able to fix this by editing the file /Library/Frameworks/Mono.framework/Versions/Current/lib/mono/xbuild/Microsoft/Portable/v4.0/Microsoft.Portable.CSharp.targets, finding the PropertyGroup that sets
And to it, adding the lines:
MonoTouch smcs /Developer/MonoTouch/usr/bin
Found this hint via http://stackoverflow.com/questions/12041290/monodevelop-is-it-possible-to-switch-pcls-compiler/12062589#12062589 and https://bugzilla.xamarin.com/show_bug.cgi?id=5329 - wish I'd found it months ago (note to self - don't give up so easy next time!)
For Mac newbies, note that this file is in the root from the hard disk (not from the user) and that you will need to edit file (and folder?) permissions in order to edit it - you can do this from finder using 'more info'.