Warfighter mod? Or mobility issue?

I love the warfighter split and love everything behind the Tier System. However, everytime I go to implement it (or really any form Of a 3xFullbody style split) my body feels like it starts to fall apart. Primarily, I start to get horrible bicep tendinitis and pain in my left shoulder when we start combining back squats and any pressing movements on the same day. With that I have 3 options….

I seem to do well if I move the exercises around from the first 2 strength days of the week to be more of a lower day on Monday, then an upper day on Wednesday, then keep the total body day the same as prescribed on fridays. I know this bastardizes the tier system but seems to let me get the prescribed training in, with its intent, without pain.
Just Sub out back squats for belt squats/SSB/front squats. Not against this idea if you guys think it’s best to keep the tier system in check, over keeping the BB back squat in.
Don’t be a little b$&ch, focus more on mobility in the shoulders and push through. It’ll solve itself over time? Also may not be as big of an issue with the current fortify programs conjugate variety on squats🤷🏻‍♀️.

Thoughts? I truly feel like this programming is dialed for exactly what I need, but the aches and pains with application seem to be holding me back. (Also for reference, been training for a little over 15 years. Coming from a couple years in a west side barbell conjugate upper/lower style of training).

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