This is my stomping ground. We lived in Lyons for 18 years before moving to Vegas (our CO house is still for sale
)
After the museum visit the best way is to from Boulder to Estes. From Boulder/Museum take Hwy 119 through Boulder Canyon to Nederland and then to the Peak-to-Peak (hwy 72 to hwy 7) to Estes. For the return you have three choices:
Estes to Loveland on Hwy 34 Big Thompson Canyon. The narrows sounds great with a Cobra open and side pipes. I can attest to this as it was my favorite drive.
Estes to Lyons via Allenspark (back on the P-P part of the way and then down the south St. Vrain canyon to Lyons (note, you're doubling back)
Estes to Lyons on Hwy 36.
All of these roads (Hwy 7, Hwy 34, Hwy 36) have been rebuilt after the 9/11/13 flash floods that wiped them all out. 36 just reopened new but alas, I didn't get a chance to drive it. Hwy 34 (Big Thompson) flooded out very close to when it did in 1976. By the time you go the road beds should be clear of construction debris.
Enjoy!