I've been an athlete for a long time... long enough to know that one of the easiest ways to injure yourself is to do too much too quickly. However, I'm also an unreasonably optimistic person. I figured averaging 50 miles a day would be alright, knowing that I'd get about 1.5 rest days after the first 6 days and another rest day every other week or so.

A surprising amount of people lived in the Kootenai National Forest; the section of trail just before Whitefish

In the last two days of the Canada to Whitefish, Montana segment, my knee started to give me some warning pains.

If I had to do it over again, I would change some things:

Plan for a less-than-average pace for the first week - Between pack adjustments, last minute sight-seeing, and getting used to biking with a 50-60 lb. bike, you will want to plan for some shorter days. If you've been training for this (with weight), obviously you know what you're getting into. But if you're like me and spend most of your pre-ride time figuring out how to do the damn trip, you probably weren't training too much.
Be more diligent about stretching/strengthening every day - The best way to avoid injury is to diversify your workouts and make sure all your muscle groups are getting activated. It's REALLY hard to do at the end of a long day of biking, especially in inclement weather, but there's no excuse for prevention.
Ride without a schedule - Don't get me wrong, I'm super grateful for all my riding buddies along the way, but I know that it would be easier to adjust for on-the-trail changes if there were no deadlines. Even simple things like "hey this lake is really cool; let's hang out here for the rest of the day" become more attainable if you don't have anywhere to be in 5 days. Maybe this sounds obvious as well, but coming from a fast-paced, hard-working, deadline-riddled life on the East Coast, this is a new concept for me.
Start with flat-clipless pedals - It's a fairly common fix for people with knee pain to ride with flat pedals. It allows for the foot to go wherever it wishes to allievate knee pain. I wish I would've started with the pair I had laying at home instead of paying to switch later.

Fortunately, while in Whitefish, I was able to see an awesome Physical Therapist, Jay Schraver. He helped diagnose me with a standard case of over use and a slightly errant patella. So far, my stretched and taped knee is feeling better.

Getting taped up at Northern Physical Therapy

I also visited Glacier Cyclery and got some flat-clipless hybrid pedals so that my foot could go wherever it wished to alleviate pain.

Glacier cyclery was really awesome when I stopped in. Recommended!

With another day of rest and making some adjustments to make my ride more efficient, I'll hopefully be back on it.

In the meantime, I ate way too much in Whitefish and soaked up the comforts of civilization with some warm showers, big breakfasts, I've-cream, non-camp coffee, and beers with friends. In the realm of bikepacking, taking just 48 hours off from biking feels like an eternity and a supreme luxury.

Bikes stand waiting while we sipped beers by Whitefish lake

Bikepacking Blog

Rest Days and Switching to Flats