To receive a research visa for India, you will need to provide either your bonafides as an independent scholar, or evidence of your affiliation with a local research institute. Working out affiliation details can be difficult. I started by making numerous web searches to identify faculty working my area in Jaipur and Delhi. After locating faculty with research interests similar to mine, I read all the publications by said faculty that I could find. This was instructive, and led me directly to a department and 1-2 faculty members at JNU that I would have liked to work with had they been in the U.S. At this point, I sat down and sent a dozen e-mails and made a dozen phone calls, trying to track these faculty members down to talk about research affiliation. It was a long and stressful process, made all the more so by my poor Hindi. I had several e-mail conversations, sent copies of my research proposal, my CV, talk to admissions on the phone, all of this. However, I think it helped me in the end, if only because I could put in my Fulbright application that I had made appropriate contact with faculty at a research university in India.*
Of course after this, a lot of the affiliation details are then handled by USIEF if you are a Fulbright-Hays DDRA student. Still, once you arrive in India, you will need to take care of paying your affiliation fees and registering as a day student/research affiliate yourself. This post will go over the steps for a JNU affiliation. I'm assuming you've made contact with your faculty advisor, and you just need to go through the formal registration process.
I will be referring to this map of JNU campus.
To arrive on the JNU campus, there is only one open gate, the Main, or North, Gate, off Bara Gangnath Marg (Road). Go through the gate, past the Dakshimpuram dormitories on the left, and take the first major left. Take another left, and this brings you onto a sort of ring road. You are headed to the Admin Building (also labeled "West Wing"), or Bldg. No. 2 on the JNU map. The entrance is on the west end of the building.
In the Admin Building, go to Room 20 (to the right). Ask for Satendrji. You will sit down at a table and go over the registration process with him. For this, you will need the following:
Your Letter of Admission from JNU
Your passport and research visa
A statement of medical clearance (I didn't have this, but I was fine without it)
A photocopy of passport and research visa
Four (4) passport photos
$100 USD (roughly INR5000) per semester of affiliation
Satendrji will give you a form to fill out in quadruplicate. He will then send you over to Room 13 to pay your affiliation fee. The cashier booth is just to the left of the door of Room 13. The Cashier will give you a receipt. Hold on to it. Sit and fill out the four forms in quadruplicate, and take them back to Satendrji. If he approves, he will cross out certain superfluous items on the forms, and stamp/sign them. Then he will send you to get a signature from the Dean of Students Office, as well as the signature of the Administrative Officer in your affiliating department. While you are out getting these two signatures, you will also need to make a photocopy of your cashier receipt.
Here's my advice. Go to the Dean of Students office (Bld. No. 13 on map) first. You want to turn left out of the Admin Building. The walkway leads past a science building and something that appears to be a greenhouse/nursery area. The Dean of Students office is behind the Molecular Sciences building. Make sure you do this before 1:15, otherwise everyone will be out to lunch. In theory, the guard at the door will be able to get your papers stamped. If this doesn't happen, you can do what I did: during the middle of the lunch hour, walk right into the Dean of Students office, say you think you need his signature, and see what happens. It worked for me, but I'm pretty sure I broke a number of rules doing it this way.
Most of the academic buildings (Social Sciences I & II, School of Arts and Aesthetics, etc.) are lined up behind the Admin Building (see Bldg. Nos. 40, 45, etc. on the map). They are much easier to find than the Dean of Students office. Your advisor probably arranged an appointment with you, so you can get your signature then. Otherwise, you can go to your discipline's building and try to find the approved Administrative Officer and request a signature.
As you are walking around, you will probably see dhabas and bookstores. There is a good range to the east of the library of this sort of thing. There are also two photocopy shops here. Photocopies as of right now are 1/2 INR per copy, so you'll probably have to buy two copies of your cashier's receipt, because who has 1/2 rupee change?
Once you have the signatures, leave the appropriate copy of the form with your department. Drop the Admissions Branch form and the receipt photocopy back in Admin Building Room 13 with Satendrji. Go back to the Dean of Students and drop one of the forms in the small box inside the entrance (to the right) labeled "Day Students". The yellow form is yours to keep.
That's as much detail as I can remember. JNU is a beautiful campus, so you might want to plan to spend the day there, watching birds and reading in the jungle. It's unlikely you will be able to catch an autorickshaw near the Admin Building. You can either take the bus back to the main gate, or you can walk, which takes about ten minutes, max.
*I am affiliated with JNU. Other options in Delhi include Delhi University, Maulana Azad Medical College, Centre for the Study of Developing Societies, and Jamia Millia Islamia, among others.