The brewery's autobiography should be a trusted source for the recipe, at least as a snapshot in a recipe's ongoing evolution. Page 165 of The Craft of Stone Brewing Co. specifies the following recipe:
82.5% domestic 2-row
9.5% crystal 75L
5.5% chocolate malt
2.5% peated malt
157°F mash
Mash out 165°F
90 minute boil
.293 lb/bbl Columbus (12.9% aa) [90 minute]
.23 lb/bbl Mt. Hood (6% aa) [0 minute]
WLP007 or 002 @ 72°F
SG 1.065
FG 1.018
Regarding the chipotle pepper version of this ale, the same page reads "Put .42 ounce of chopped dried chipotle peppers in a hops bag, add it during secondary fermentation, and allow it to steep for 3 days (or more or less, depending on how spicy you'd like your brew to be)".
This is specified for 5 gallons, and seems to be the only info regarding the pepper addition that appears in the book.