September is a fantastic time to be there. Late September gives you the golden aspen trees but also the possiblity of worse weather. Early september doesn't give you the spectacular color changes but is warmer and snow is less likely.
Once you get into the Rockies, it's hard to find a bad
route in CO so finding a good one is easy.
As for a central location, I would recommend Buena Vista, Leadville, Dillon or Breckenridge. From any of those locations you have good paved MC roads in all directions.
As for "must see" rides, really you could spend a Month on Colorado and not hit them all. A few to consider (in no partiuclar order) are:
* Independence Pass (CO 82) between Leadville and Aspen. This is the 2nd highest continuous paved road in the US.
* Trail Ridge Road (US 34) in Rocky Mountain National Park. This is the highest
continuous paved road in the US.
* Mount Evans rd (CO 5). At 14,125' this is the highest paved road in North America, possibly the highest paved road in the Western Hemisphere (don't know if South America has higher paved
roads or not. I know it has higher unpaved
* Loveland Pass (US 6) between Silver Plume and Dillon
* Monarch Pass (US 50) between Poncha Springs and Gunnison
* McClure pass (CO 133) between Carbondale and Paonia
* CO 92 between Hotchkiss and Sapinero.
* Unaweep/Tabegauche Scenic Byway (CO 141) between Naturita and Grand Junction.
* Lizard Head Pass (CO 145) between Telluride and Dolores.
* Wolf Creek Pass (US 160) between South Fork and Pagosa Springs
* Slumgullion Pass (CO 149 between Gunnison and South Fork.)
* Red Hill Pass/Million Dollar Highway (US 550) between Durango and Ouray.
and one "out of the way" but very fun recommendation:
* Douglas Pass (CO 139) between Fruita and Rangely.
Obviously, I've left a lot of them out, but really all you need to do is get a good map and then figure out where you want to go - even the "worst" road in CO is likely to be better than the "best" MC road out in the flatlands.
One thing: Be prepared for Winter conditions year 'round. It's been known to rain/snow/hail on top of Mount Evans or Trail Ridge even in July. Cold Weather gear is a must no matter what time of year you are riding in CO. And if you are planning on going over passes higher than 11,000' or so, it's better to "summit" them in the morning as afternoons tend to bring thunderstorms. Being above treeline, you will be a target for lightning which kills a lot of people in CO each year.
Remember also that September is the start of the rutting season for deer and elk so you have to be careful of animals on or near the road. Best advice IMO is to plan your riding so you are NOT riding after dark (and why would you want to, anyway? You'll miss the scenery!)
EDIT: Here's a pic of me near the top of Trail Ridge Road in early September, 1999. Notice how cold/wet it looks!