What is the procedure to get transcripts from MUHS, Nashik? Do they send transcripts directly to WES for the ECA? Is there any agency that can help me through this?

In order to get transcripts from MUHS Nashik, you need to visit the college. You will be required to submit an application letter stating the reason for the transcript. A DD will also be needed as per their fee structure. 

The process to get your transcripts can be tedious. Applying through Mail Transcript can be a good alternative. They will only ask for scanned copies of your mark sheets and degree certificates. Everything else is taken care of by them. One of my friends applied through this organization and they helped her to send transcripts to WES direct shipment from university.