Coming back to the program. Need suggestions about substitutions

I have been injured for a while with a SI joint issue that has prevented me from deadlifting and even squatting on some days but have finally gotten better to the point that I can atleast squat with no pain. I am going to restart the program again from week one day one. My question is I. The interest of saving my joints and making maximum progress I was hoping to substitute some of the sessions which has you do pyramid squats at 70% with varying reps. I read on the forum that Boris utilizes this with newer trainees in the interest of increasing mass so I feel I would benefit more from subbing this for the movement with a different rep scheme. Or even maybe a variation like paused squats. Can anyone chime in to a sub I may be able to use?

If you want to remove the pyramid squats you have a few options. If available, you could do squats with chains or bands, to increase leg strength. If you want to improve overall technique, you can do Pause Squats. And if you want a decent training effect through using lighter weights, try a front squat (Which will also help to correct forward lean on your competition squat.)
 :)

You could try doing the pyramid with a reduced intensity of 5-10% perhaps, it really depends on the injury.