By "best" I'm not sure what you mean. Fastest, shortest, most scenic? But if the destination is foremost I'd follow a Mapquest or Google route, which is mostly interstate the first day.
As for a stopover, I'm sure Flag has some nice places, but 30 miles west of it is Williams AZ. Very easy on/off and a clean newish RV park we've stayed at. It's the Grand Canyon Railway & Hotel. It's a short walk to a couple of eateries. Rod's Steakhouse is a tad over priced, but good the last time we ate there. Across the street is a nice cafe, more on the diner side. I'm assuming both are still in business.
As long as you see 18 wheelers on the roads you're taking, I can't imagine having a clearance problem. But money spent on a trucker's atlas will be worthwhile IMO. They will identify low clearance structures and just generally have a lot of useful information not found in the $5 Walmart books. At least they used to be $5!
From Flag you can either go north and east to Four Corners, or continue on I-40 to Gallup, NM, then north to Cortez and Durango. I've done both. Once you leave I-40 you're not going to find a lot of services if you have a breakdown, and so I prefer running on to Gallup if I'm towing.
Two days is very doable and should not be too wearing on you. Enjoy Colorado and be safe.
