Can you apply the 5/3/1 progression to your own split like upper lower?

Absolutely!

The 5/3/1 progression is a great way to structure your workouts and can be applied to any split. For an upper/lower split, you would do 5 sets of 3 reps for each exercise in the upper body workout, followed by 5 sets of 1 rep for each exercise in the lower body workout. This progression allows you to gradually increase the weight and intensity of your workouts over time.