Gboyd, I figured this would be the best place to post my results since it was discussed here. I chopped the chipotle peppers up and dried them sauce and all. Then I chopped the jalapeños and the tomatoes and dried them too. I just placed them in a pan in the oven on warm overnight with the door cracked. In the morning they were very dry and were easy to grind up.
The jack recipe went well but it was a real challenge pressing 4 different cheeses at once. Tried several things that didn't work and finally just started alternating them; very less than ideal pressing. But... they turned out very well aesthetically. The pics posted show the 4 pepper jacks: (in this order) chipotle, pepper/tomato, pepper plain and a big Manchego (from last week)in the back.
I probabaly did not add enough jalapeños to the third one. You can tell from the pics how much I added for what would be approximately a 6 gallon batch because the whole batch was 25 gallons and I just unscientifically divided the curd at the end. Hope others can learn from my mistakes.