Sounds like a great trip - I'll be right behind you finishing Gunsight on the 4th and in a similar situation.
I'm going to reach out to GNP once the respond to my current email regarding Pete's parking restriction comments. If you can't park at Lake McDonald due to not having shuttle tickets, perhaps instead park at Logan pass and shuttle down to Jackson Glacier Overlook on the St. Mary shuttle (which I understand you have tickets for), and then on the last day, shuttle up to Logan. This avoids a shuttle connection at Logan.
Keep in mind, additional shuttle capacity (25%) opens 48 hours in advance. There is also the chance that shuttle occupancy restrictions go away as conditions approve. I wouldn't bet on either of them, but have them in your back pocket as a way to 'improve' as the dates get closer.
All that said, it looks like there will be 'connections' at Avalanche (which I think there always has been) and Sun Point (which I think is new). My experience at Avalanche was that you had to get off if there were people waiting to go up (if starting the shuttle at Apgar). The other concern is that they are metering people very specifically with the ticket intervals, and explicitly say to contact staff in advance if boarding somewhere other than Apgar or St Mary (inferring open seats probably won't be available without coordination). Trying to catch a bus at a specific time coming out of the bush isn't a fun strategy.
If visitors plan on boarding at an en route stop (i.e. Lake McDonald Lodge, Avalanche Campground, Rising Sun, or the Rising Sun Boat Dock), they must communicate to transit staff during their advanced check-in at the Visitors Center, to ensure seats are saved for them.
I also just spotted this one today:
A limited amount of walk up tickets will be set aside for visitors without smart phones, credit cards, or e-mail accounts.