It's been awhile since the original post, but hopefully I can spare someone else the time I took on this.
Some things will not covert cleanly when cloning p2v.
After some testing, I found that none of the above problems occur when cloning v2v. So, for me the solution was to work with v2v only. My conversion to a virtual environment is complete so I don't have to deal with this anymore, but my lesson learned is to convert one, correct as above, and then on do cold clone v2v after that.
Many thanks for the info/suggestions.