Place chipotle peppers and adobo sauce in blender or food processor and give a little pulse, adding a splash of water as necessary to make a bit of a paste (or you can finely chop if you prefer)
Add all chili ingredients along with peppers to crock
Cover and cook on low for 7-9 hours (the longer you cook the better the flavor)
Remove chicken and shred with 2 forks, return to crock
Melt butter in saucepan over medium high heat on stove
Whisk in flour until smooth
Slowly add milk while whisking to make a smooth sauce
Continue whisking over medium high heat as you bring the sauce to a simmer and it thickens enough to coat a spoon (about 3-5 minutes)
Remove from heat and stir in shredded cheese until smooth
Add cheese sauce to crock and stir to combine well
Notes
I cooked this in my 4 quart round slow cooker for 8 hours.