Denise,
you raise very good questions. I will do my best to answer them so they make sense.
First off, cancer staging and diagnosis is a complicated thing and oftentimes it can't be correctly staged until either a biopsy or resection and subsequent pathological exam of the tissues is performed. Typically what they mean by "clear margins" is that they have a centimeter, at least, of clear, cancer free tissue. Tumors have tentacles, much like an octopus, so it is vital to have clean margins. 3 weeks does seem like a long time to get a pathology report and a consult from the doctor, but consider that most of us, even fast tracked, took 4-6 weeks from Dx to start of Tx. See this link for the difficulties and complexities of this particular and rare form of cancer:

http://www.oralcancerfoundation.org/facts/rare/mc/index.htm

Here is another link further demonstrating the complexities of MEC:

http://www.thedoctorsdoctor.com/Diseases/mucoepidermoid_ca.htm

Lymph nodes: They are fairly straight forward to palpate - if they are cancerous they will be enlarged, firm and typically have an almond shape to them.

Pet Scan issue: A PET scan at this point would present many false positives due to the healing going on.

You are fortunate to be at MSK with such a rare form of cancer. They are the highest rated Comprehensive Cancer Center in the US and probably the world.