I've gone ahead and built 3 MU plugins...one for my custom post type, one for the taxonomies, and one for meta boxes.
By putting the plugins in the MU folder, I can get all of these to appear correctly on the main blog and all sub-blogs. But, I'm having two problems. First, the data isn't saving right. Second, the custom field information isn't showing on the post.
Without getting into all of the code, let me first ask if I'm going about this the easiest way. I don't know of any plugins that will create a post-type with custom fields throughout a multi-site network.
There a re quite a few to create them for one blog, but not for all of them.