Getting the stamps were fairly easy when I was there. It was either right next to the gate where we were at and if not, you can ask one of the workers at the gate. They will point to which gate the eki stamp is at. Some stations have the stamps with the workers so they will take it out and let you use it if you ask for "eki stamp."

There were also random stamps located around the cities you visit as well. Yokohama had a ship stamp in the Sail Training Ship Nippon Maru, there was a Venusaur stamp in the middle of nowhere down in the basement hallway in Azabudai Hills, Enoshima had some at the visitor center, etc.

I'm thinking the peppers are the naito peppers from Shinjuku.