So, I did 2 years at Western University in Health Science, and after a 2 year hiatus, I'm planning on transferring into PNB at McMaster for Sept. 2015. I've already gone through the application process for that, and ordered all my transcripts, ect.

However, I'd also like to take a physics and a calculus course in the summer via McMaster. How do I apply to do that?

Do I use the "letter of permission," even though I'm technically not in a program right now? Would I still have to go through Western to get the permission?... Is there another option I'm missing?

You should contact the registrar at Mac first. Technically you are not a McMaster student until September, but they may be able to allow you to register in the summer, and if not then you will most likely have to go through Western. The "letter of permission" from Mac is for Mac students wanting to take a course at another school, so you definitely don't fall into that category.

I think you may be treated as a continuing education student or a "mature student." Definitely contact the Registrar's office though to get all the details sorted out before you have to sign up for courses (which opens up in March).