I know the Penobscot well. I have the former incarnation, the Canadienne. I agree tandem is probably better in Class II-III if both paddlers are skilled. I also agree with LOTS of flotation - bow, stern, center. Pumphouse at lower levels has not been a problem for me with those kids of boats. I don't think you'd make it at present levels. Anything from 700 -1,400 cfs there should be OK.
I have seen boats like yours do Filter Plant on the Poudre, but you need to know what you are doing. Always have some safety boaters along.
When I first came to Colorado all I had was the Canadienne, but it didn't take too long before I realized I needed a true whitewater canoe to get the full benefit of the rivers in the region.
I also recommend that you find a local canoe club - Poudre Paddlers, Rocky Mountain Canoe Club. They will get you to new rivers and provide lots of support.