I don't know what restoring to MK1 defaults does, to be honest.
OK, that's good that you're saving to a separate drive. So, check this out...
Logic/EXS uses Spotlight to index the locations of samples, or so the story goes. Now, the EXS instrument itself (not the GUI/front panel but the part you see when you access the EXS instrument editor) contains references to the samples which the instrument needs. The instruments themselves can only live in one location -- the Sampler Instruments folder on your main HD. However, samples can live anywhere. So when Logic loses its mind in trying to load up EXS samples, what's happening, I believe, is that the name of each sample gets looked up by Spotlight to find its location. And...
...because you've saved and re-saved the samples so many times in all of your various projects (by having the EXS samples box checked when you save), Spotlight now has this huge number of options to choose from as to which of those copies of each sample it's going to load up.
So one way you can stop this from happening is by re-indexing your drives, and in doing this, specifically excluding your project drive. This way, Spotlight will keep its nose out of your projects, and thus, won't keep finding all those multiple copies of the samples. It will likely then have only one choice as to where to find those samples: in the samples folder (located in the same directory as the sampler instruments folder).
I'll post back later with the procedure to re-index spotlight. But in the meantime, I'd like to emphasize what I said before... that unless you need to make your projects "portable", it's not necessary to save your projects with any EXS assets at all because they already exist on your system in their original locations.