Hi Jeremy,
That's quite the road trip you've got planned!
You're probably aware, but just in case you aren't.....Colorado had a big snow winter. Most of the high mountain trails are late opening this year. Some may not open at all. Let us know if you need sources for such info.
Having said that, the following is based upon the assumption that all trails are open.
For me, the Alpine Loop, while amazing, is a popular route marketed to the tourists. Most folks will travel it in a day or less. In my opinion, Engineer is the better of the two trails that make up the loop. If I was going to spend 2-3 days there I might consider making a loop out of Engineer and Stony Pass (instead of Cinnamon). I see the latter as much more of an overlanding route. You've probably never heard of it because it isn't promoted because of it's length and location compared to the nearby towns.
https://www.trailsoffroad.com/trails/467-stony-pass Be aware that the Pole Creek crossing can be quite deep after rains or during peak snow melt season. As for the latter, try to cross it early in the day so the levels will be the lowest. There was recently loss of life after a couple crossed it in the morning successfully, but then found it too deep on the return. The levels should be much lower by August.
I also recommend you spend one of your days running
Imogene Pass perhaps making a loop out of it with
Ophir Pass. Consider also
California Pass,
Hurricane Pass, and
Corkscrew Pass which makes a good connector between the highways.
I know it's probably more than you're looking for, but consider joining us for the following:
Rocks N Rockies. We'll start in Moab and end up in Ouray.
I'll leave you to chew on that a bit. Let us know what else you need.