Okay here is my best attempt to list everything place on the CT that is exposed to lighting danger. I use major landmarks like passes for easy reference. An exposed area may start slightly before or after a major landmark. Distances are my best estimate using Hillmap.com of how much trail is actually above treeline.
Note - You are responsible for your own safety here! I list even marginal sheltered spots just so you know were they are in case of an emergency. Use your head!
When I say a places is okay in "marginal weather" I mean this. "Marginal Weather" means a thunderstorm is possible but I expect to have 15-30 minutes before it gets really bad to find shelter. I would not start hiking across Snow Mesa in "Marginal" weather for example.
Here are all the high and exposed spots from North to South.
1. George Pass - 1.5-2 miles above treeline
2. Ten Mile Range - 4 miles above treeline, no bail out points, very high and exposed in places.
3. Searle Pass to Kokomo Pass Area- 4-5 miles above treeline from Guller creek to basin below Kokomo Pass. Willows at the top of several small creeks are a spot to hunker down in an emergency (only in an emergancy!).
4. Holy Cross Wilderness - 3-4 miles in sub alpine forest with one two ridge crossings above treeline. Dangerous area in thunderstorm, bail out options make it okay in marginal weather.
5. Collegiate Peaks Wilderness (northern section) - Trail close to timberline at times. Mostly safe except during a bad thunderstorm, quick bail outs.
6. Collegiate Peaks Wilderness (southern section after North Fork Cottonwood Cr) - Saddle in trees not exposed. For great view walk through trees to open ridge to the east (not on trail).
7. Monarch Pass Area - 3.5-4 miles above timberline in two sections with a forested saddle in between.
8. La Garita Wilderness Part 1 - 3-4 miles above treeline starting at Cachetopa Creek headwaters. Trail briefly enters forest again at the end.
9. La Garita Wilderness Part 2 - From treeline the trail climbs up for about 1.5-2 miles to San Luis Pass. Trail is very exposed. Bail out option at San Luis pass, forest is just to north down overgrown side trail.
10. La Garita Wilderness Part 3 - San Luis Pass to East Mineral Creek Headwaters, very high and exposed for 2-3 miles.
11. La Garita Wilderness Part 4 - East Mineral Creek to West Mineral Creek Headwaters, CT goes over two small passes above timberline, briefly in trees at the top of each drainage.
12. West Mineral Creek across Snow Mesa - 7-8 miles no trees, very exposed in places.
13. Jarosa Mesa to Big Buck Creek headwaters - 6-7 miles, no trees. Trees at headwaters of Big Buck Creek (I believe there was a Yurt around here too).
14. Ruby Creek Headwaters to Carson Saddle - 8-9 miles, no shelter, high and exposed, do not do this if the weather looks bad. At Carson Saddle a dirt road leads down to treeline (not on trail). Stealth campsite in willows above trail on right. Note this willow campsite is is the best campsite I am aware of between here and Elk Park. It is not perfect but the willows provide a bit of a wind break and its probably one of the safer places to camp above treeline.
15. Carson Saddle to Elk Park - 20+ miles, no shelter, some places very exposed. Look at a map for possible exit routes if weather gets bad.
16. Molas Pass to West Lime Creek Headwaters - Trail stays close to treeline for the most part. Avoid in bad weather but bail out options make it okay in marginal weather.
17. West Lime Creek Headwaters to Rolling Pass - 3-4 miles, no shelter until the basin below Rolling Pass.
18. Grayskil Creek to Bolam Pass - 1-2 miles above treeline. Most exposed on Rolling Pass.
19. Bolam Pass to Blackhawk Pass - This whole section is tricky because you are either close to treeline (below Harmosa Peak) or walking a narrow ridge that is exposed whether you are technically above treeline or not. Its not as bad as some of the other areas but if a thunderstorm started I'd probably stop at the first good spot and wait it out.
20. Blackhawk Pass - 1.5 miles above treeline. The creek south of Blackhawk Pass was the last water between here and Kennebec Lake when I finished the trail in September of 2012.
21. Indian Trail Ridge - Trail follows high narrow ridge. Forest ends south of Cape Good Hope Trail. Some parts of ridge very exposed with no exits but it is possible to go down from several saddles to the west.
22. Kennebec Pass Area - 3 miles mostly above treeline. Some trees in basin. Last above treeline spot before Durango.