I am in a similar situation myself.
What I've been doing is starting with premixes and/or skipping chapters. I haven't started XTrain yet but with workouts like Trisets or Lower Body Blast, I pick a shorter premix and skip through certain exercises that I know are going to be too much on my body at this point (walking lunges come to mind).
Another thing to consider that I've found quite beneficial is doing the lower body work without weights. The only exercises in Trisets that I do with weights are the various squats and the deadlifts. Otherwise, body weight is plenty. I still feel the burn but I don't exhaust myself aerobically/anaerobically so I can continue with the workout. It's allowed me to modify the pace without changing the pace if that makes sense. I'm also using lighter weights for all muscle groups and SLOWLY increasing them. I was never one to pace myself with increasing weights as I could always do it. Right now however I'm perfectly fine taking things slow and my body is still getting a great workout. I don't think the premix matters so much as does the time and how intense you make it (or don't make it). Changing up the premixes whether it be a different one each workout or sticking to a certain one for a period of time will only benefit you regardless of how you use them. By changing them up, you add variety which helps you physically and mentally by keeping things different.
Another modification is not to do Cathe's cardio and focus on the strength workouts until you build up the proper endurance. I don't use her cardio workouts anymore bc they flare my FMS but I do know that back in the day when I did Cathe's worouts for cardio and strength, I cut the cardio out and opted for more moderate forms until my body became adjusted. Whether it was injury or illness, there were times when I needed to dial back the intensity and pace. In doing so, I was always a few beats behind Cathe and crew so I instead used other instructors DVDs or walked. That's what I'm doing now for cardio- Leslie Sansone and when the weather improves, outdoor walking only. Cathe's Strength and Walking are my two loves so I combined them and I'm loving every minute of it!!! But that might help you too, saving the energy and stamina for the strength workouts which over time will make you stronger and help improve your endurance to do the advanced cardio that Cathe is known for.
I plan on sticking to the total body workouts as that's where my interest lies at this point, however when I do get into XTrain, I'll do the same thing: premixes with lighter weights and slowly build up the time and weight as I go.
...I'm also just getting back with it after double knee injuries (and multiple other layoffs over the years..work...life..yaknow