I had pretty severe Tendonitis in my knees. For a while I thought I couldn't squat or do much lower body exercises. Eventually, I found out that the Tendonitis was due to a muscular imbalance within my quadriceps group. Ever since I began to correct the imbalance my knees have not flared up. I would suggest focusing on primarily strengthening the stabilizing muscles in your shoulders before you keep trying to avoid the pain with alternatives. Also, I have always had shoulder issues with pressing movements while using barbells, Im sure you've already done this but if I were you I would strictly stick to dumbbell pressing movements. I do not think the length of your femurs can hinder your ability to squat or deadlift unless you have a serious medical issue. I would not take those two main lifts out of your training.