what exactly am I supposed to do with these things? -besides sell them-

you can use them at vending machines or to buy things from the token shop when it stocks.

you can Also use them to Zap your pets into a different spieces/give them stats/gender change them.

I see, so when exactly does the Token Shop stock? Or is it random?

It's sheer random

Dang. Does it restock often though? Or is there a huge gap in between restocks?