Matt:
Thanks for writing in with your question. Scott Semple is spot on and I think your idea of subbing a bike ride is totally acceptable. First and foremost in any training program is injury avoidance but whatever means necessary.
Here are some additional thoughts that might help you in both your guiding and training.
Unless you’ve got a for sure orthopedic knee problem, like cartilage or ligament damage there is a very good chance that what you are experiencing is what is called patella-femoral pain, runners knee, jumpers knee. The pain you feel in your knee in this case is the patella being pulled out of alignment, typically by a tight IT band of tight vastus lateralus (the lateral/outside quadricep).
A very simple test is to do some extended (like 10min/side) rolling either on a ball or foam roller on the lateral quads and see if that doesn’t make you knees feel better. If it does then you need to do this more often as maintenance. Especially after a guiding trip and before your runs. You are suffering from an over use injury related to your job of carrying heavy weight downhill.
Next step is to make your legs able to handle this load better. My experience with guides is that because you are doing a very physically demanding job you probably don’t do much if any general strength training. Despite being on your legs and carrying a heavy pack, your legs are not strong enough (strength reserve) nor do they have enough local muscular endurance to allow you a good margin between what you can do comfortably and what your job demands. Here is what I would recommend as a longer term program that will make your legs bullet proof for both running and guiding: Add one session of our ME progression . I’ve used this with many alpinists, guides and mountain runners with great results. It will make your legs tired but I suspect your guiding day can me done with some residual muscle soreness and fatigue. It will greatly improve the fatigue resistance of your legs and should help reduce the knee pain when combined with the rolling.
In the off season when you have more time to allot to training I’d add in a max strength gym session (4-6 sets of 4 rep at 90% of of one rep max) that includes Bulgarian Split squats, Box steps offs/heel touch, Box step ups.
I hope this helps.
Scott