If you say the fudge you had was smooth (no pieces), I think I would puree the peppers before adding them to the rest of the ingredients.
There is also such a thing as "jalapeno oil or extract" and powdered jalapenos which you might be able to use in place of the actual peppers.
Dark Chocolate Jalapeno Fudge
4 1-ounce squares dark chocolate
3 cups sugar
2 tbsp corn syrup
1 1/4 cups milk
4 tbsp butter
1 tsp vanilla
8-16 finely chopped pickled jalapeno pepper rings
Line an 8 inch square pan with foil and spray the foil with cooking spray. Alternatively, butter the pan.
Melt chocolate in pan over very low heat. Stir in sugar, corn syrup, and milk. Increase heat to medium and cook, stirring until sugar dissolves. Wash crystals from side of pan. Cook to 238F on candy thermometer (soft ball stage). Remove from heat, and without stirring, add butter.
Cool to 120F. Add vanilla and jalapenos and beat until mixture begins to thicken. Pour mixture into the pan and cut into squares when cool (room temperature).
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Dangerously Spicy Chocolate-Chili Fudge
1 lb high-quality dark chocolate, chopped (I used Lindt Excellence 70%)
1 Tbsp unsalted butter
1 tsp ground cinnamon
1/2 tsp ground cayenne
1/2 tsp ground nutmeg
1/2 tsp salt
1 (14-oz) can sweetened condensed milk
Butter the bottom of an 8-inch to 9-inch square baking pan, and line with a square of parchment or wax paper.
Put ingredients into a metal bowl set over a pan of gently simmering water, and stir the mixture occasionally to melt. It's going to be very thick. Spread mixture into the pan and chill until firm (or overnight).
Run a warm knife around edges of pan to loosen the fudge block and flip it over onto a cutting board. Remove the paper, and cut the fudge into 1-inch squares.