Mike Brantley has done a few YouTube videos for both AmigaOS4.x and MorphOS running Lightwave3D, VistaPro and a couple other Amiga 68k applications. Some of them (like Lightwave3D) need to have their screens promoted, using something like ModePro, to get them to work.
He is the guy I would try to get in touch with for info on the tricks to getting 68k programs to run on MorphOS best.