What are you using to compile? VS? You will have better luck if you compile the mojoportal.mds using MonoDevelop.
I have not done any testing with compiling on Windows with VS and I don't think just using the MONO compilation directive will make that work. The MonoDevelop solution leaves out some files for things that are not yet implemented in Mono.
Also the Lucene.Net.Lockdir setting is not needed on Mono as far as I know its only used in Medium trust and there is no support for medium trust or Code Access Security yet in mono.