Where to get thses diff parts from?
 

I need both axle boots

axle seals

and circlips (what are these anyway?)

So where is the best place to get these?

I'd try Rosenthal Mazda. I've dealt with them many times and have had nothing but good experiences. The circlips go on the ends of the axles that insert into the differential. They are what holds the axle in the diff.

Ok, they arnt open so I emailed them. Anywhere else?

I usually start with the Miata.net marketplace. There are a few dealers in addition to Rosenthal who are usually within a few bucks of eachother on everypart. You could also try Autozone or Napa

onlinemazdaparts.com

I've purchased OEM parts from a few dealerships, and generally speaking, these guys have had the best prices. A big plus for me is that they are in Charlotte, so shipping is quick for me.

Can I even buy just the axle boots? It seems everyone sells the whole cv joint for like $60.

Yes, you can buy just the boot. Places like O' Riely's and Autozone usually have different size boots in stock. They can usually pull out the book and look up the right ones if you know the outer diameter of the different ends of the boot.