Welcome to CNH! This is your new best friend right now lol!
What you found was either a mating plug or a heat plug. Either way you are probably right that she is pregnant and due any day now (gestation is 111 days).
No you did the right thing in seperating them now. Females will breed back in the days leading up to, during, and right after birth so seperating now is the best way to prevent another pregnancy. Mom and Dad should be kept seperately permanently unless you know the genetic/health background, have a pedigree, and have been shown/evaluated by a professional breeder. The good news is if you have boy kits they can live with dad and girl kits can live with mom so they will have company.
Read through the FAQ at the top of the Breeding and Babies section and see if that will answer a lot of your questions...
You need to make sure the cage she is in is baby safe - that is your first priority - the spacing on the cage bars can be no bigger than 1/2"x1/2" or 1"x1/2" or they WILL escape within hours of birth. They are climbing and jumping and running by the time they are dry or before! You will also need to get a digital gram scale so you can weigh babies to make sure they are gaining weight. If you don't already have a chinchilla knowledgable vet on hand you will need to find one and an emergency vet as well in case there are complications with the birth.
I am not sure what blocks are - are these hay cubes? What kind of food are you feeding her?
Take out any ledges that are in the shelf so that mom will stay down to nurse and keep babies warm. It also lessens chance of accidental injury.
We will also need pictures when they come