First off, Justin, those great photos, the berries, the trout, and the country you hiked thru would seem to indicate you got your money's worth, even if you didn't complete the SHR section you intended. Many trips don't work out as planned for a variety of reasons. The key is to remain flexible and take what the situation allows. You did just that, and I commend you for your flexibility. It will serve you well on future trips. As for the problem with altitude, I am a little puzzled. You don't mention having any problem with Kearsarge Pass, which higher than Grouse Lake, which makes me wonder if maybe the problem wasn't with altitude per se but one or more of the following: dehydration, the heat going up from Roads end to Grouse lake, hiking too fast. Also, if you determine that none of the above were involved, you might consider talking with your doc about a prescription for Diamox. It is pretty effective for preventing altitude sickness. Somehow, though, given that you are young, strong, and presumably at least reasonably fit, I suspect one or more of the 3 things I mentioned have a lot to do with the problem. If I were you, I would use carefully selected shorter hikes that involve ascending to 11-12K feet to experiment with hydration, pace, and building tolerance to heat, possibly Diamox, or any other variable you think might be involved, to sort out the cause of the problem before committing to a longer, more demanding route like an SHR section hike.
My 2 cents.