What is the hardware configuration of your SQL setup?
I am not sure if I understand your setup correctly. Do you mean that you have 12 mongod servers running on a single EC2 instance? Running more that 1 mongod on a single machine is definitively not a good setup for performance. And definitively a bad implementation for data redundancy, especially if you are writing on the same disk, you lose the disk you lose it all.
2-node replica set is not a recommended installation.
Where is mongos running?
How do you insert the documents? Could you please share your code? Is the insert code running close to the mongo system or remotely?
What is the total size of your input files?