What was extending your knees then?
And even if this is the case, why don't you go back to the linear progression to strengthen them? Strengthen everything else too, but which will stall first, the parts that are already stronger or the parts that are weaker at the outset?
The former ("plain old SS" a/k/a the novice linear progression) is advised. The latter (throwing hypertrophy work "into the mix") is not. Have you read the books?
When the deadlift cannot be increased each and every workout, you need to move on the Phase II, where it's alternated. The press is pretty important (crucial, some would say) for ongoing shoulder health, so I don't recommend leaving it out. I recommend actually spending a little more time with the materials because you appear to have several misconceptions. I don't mean that to sound critical, I just think you're not so obsessive or compulsive as to have read the book, perused the articles, or sought out previous discussions on this topic, and that it would be valuable for you to do so.