Plant control is distinct from customs. It has a separate desk / section at the airport - It might be signposted as "Plant Quarantine" or "Plant Protection Station," I think it's close to the health control desks (for human health) before immigration, but it might be in the customs hall....

With regard to the rules for items that you might bring from India:

General guidance (page with link to PDF pamphlet)
https://www.maff.go.jp/pps/j/guidanc...let/index.html

Detailed list for items from India (Japanese)
https://www.maff.go.jp/pps/j/search/ikuni/in.html

Almonds & Pistachios - Not listed. I believe that means that they are exempt from control.
Chocolates - Processed and packaged food product. Should be exempt from control.
Saffron - Dried spices. MAFF states "Please contact the Plant Protection Station"

If you decide to bring items and declare them to the plant quarantine station at NRT, I recommend that you purchase items that are processed (e.g. roasted nuts rather than raw) and well packaged. Items that are packaged in shrink-wrapped boxes will attract less scrutiny than newspaper cones that contain the same items.

EDIT - I see that you're bringing items from the US, not India. In that case, you need to refer to this list:
https://www.maff.go.jp/pps/j/search/ikuni/us.html

Nuts (excluding shelled Brazil nuts and shelled walnuts) Inspection required upon entry
Chocolates - Processed and packaged food product. Should be exempt from control.
Saffron - Dried spices. Not listed. Possibly exempt from control if the country of origin is the US.

[Kind of surprised about taking saffron from the US to India. I would not have imagined that.]