If you just care about getting the GPX: http://caltopo.com/m/7QSQ
If you want to read a bit of my thoughts/reasoning...keep reading.
My hope is to do a State by state write-up about possible alternates along the CDT before I leave. Today though I want to talk specifically about one of the longest alternates on the CDT the Butte Super Cutoff (aka the Big Sky variant) and the variation on this alternate I'll be taking.
The CDT South Bound traditionally will follow the divide along the Montana/Idaho border until the Wyoming border and the start of Yellowstone National Park. This section has had some mixed reviews, some indicate it has a lot of PUDS (Pointless Ups and Downs) other have indicated that because of going above treeline you still get great views so nothing pointless. My own thoughts are that it looks like you kind of end up with more of the same views you've already had in Montana and it looks like quite the rollercoaster. As I'm not exactly a purist about remaining only on the official trail, and practically no one on the CDT is. Instead, my main goal is just to see some great sights.
The Super Cutoff cuts this entire section out and takes an alternate route through Yellowstone meeting back up at the Parting of the Waters at Two Ocean Pass outside of Yellowstone. It heads through some, in my opinion, more interesting areas providing more varied scenery traveling through the Tobacco Root Mountains, Spanish Peaks, and most interesting to me is the Gallatin Petrified Forest. This route, as you can probably tell by the name also 'cut off' a significant part of the trail coming out by some estimates up to 200 miles shorter than the officer route. This works to my advantage because I want to take two alternates after Yellowstone that are longer than the official route. Which leads to my major deviation from the variant route.
I'm planning on roughly following Francis Tapon's Teton Route which instead of following the continental divide shifts west into Grand Teton National Park and makes its way to the Teton Crest Trail before some cross-country to return to the main trail in time for the Wind River Range. The Teton route is absolutely more scenic than the main divide so it is really a no brainer to head over that way and add another national part of the trip. The Teton route is also longer and potentially slower so that is one place that will eat up days I saved taking the cutoff.
There is one problem with the Teton route, though, the easiest place to branch off is in the Heart Lake area of Yellowstone which is something like 50-60miles behind where the normal cutoff route rejoins the trail. Rather than backtrack that distance after regaining the main trail I've explored some further alternates through Yellowstone that will reconnect earlier. Essentially once the route enters Yellowstone and hits Mammoth I'll be dropping south through the park instead of following the Northern and Eastern borders. I've found a two major routes of interest, one lets me reach Old Faithful which I'd otherwise be missing out on, and the other follows the edge of Yellowstone lake for a bit. I'm leaning towards doing the Old Faithful route because it goes through some animal heavy areas but the Yellowstone Lake route is a little shorter ultimately so depending on my pace (and bear activity on the other route) I may head that way instead.
I had a fair bit of trouble finding any GPX of this alternate so I've made my own combining the Onion's route (https://www.ocf.berkeley.edu/~garret/cdt/alternates.html) for the first bit from Butte to Ennis Lake then following Brian and Martina's Route (http://www.wildernesstravels.co.uk/cdt/bigsky.htm) from Ennis Lake to Mammoth where my own route takes over. I've mapped the Onion's route as a purple alternate alongside some other alternates mentioned by Brian and Martina or that I discovered that I may want to take myself.
The results of my work are available on Caltopo: http://caltopo.com/m/7QSQ where you can the GPX. Hopefully, some future hikers find this useful.
EDIT1: Another hiker has added another Alternate that connects with this but walks through Butte itself (no hitchhiking) and takes an abandoned rail line back out to the main trail.
EDIT2: I'm really undecided on following the Teton route at this point. At first it seemed like a great idea and everything I hear about it is that it is an awesome route apart from the road walk at the northern end of it. On one hand, the Tetons look gorgeous, and apparently the trail itself is reasonably maintained compared to a muddy and poorly maintained trail leaving Yellowstone on the main route (allegedly). On the other hand, the main route of of Yellowstone goes through an area where you're more likely to see a grizzly bear than another human, and I'd be missing one quintessential landmark of the continental divide: the parting of the waters at Two Ocean Pass. This isn't exactly the most amazing sight to be seen but it really represents what the divide is as at this location there is a split in a little stream. Doesn't sound too exciting but the split is on the divide itself leading to one side eventually heading to the Atlantic ocean, and the other to the Pacific ocean.
I'm probably not going to make my mind up on this until the last minute so I've taken the GPX and printed maps for all possible routes and I'll end up decided on trail