New Rules of Lifting is fine....but what next?

I need some knowledgeable advice here.

Bit of a back-story; I was heavy lifting before I started doing NROL4W. I somehow injured my knees, so I sought after a well written program and after reading so much praise of the routine on these forums and the amazon reviews, I got the book. Took some time off from the gym for cardio at home, then life got in the way so I took some time off from consistent exercise for about 3 weeks, then completed phase 1 of NROL4W. My knees are recovered (yay!) and any weight gain/strength loss from my time off has been lost and recovered.

Now that I've moved into phase 2 of New Rules, I don't like it anymore. Workout A is good, but I have to add sets and extra squats. Workout B...Hate it for several reasons, but I appreciate some good interval training. And, honestly, things that were really toned before all of this aren't so much anymore. My calves, delts, inner thighs, are all lacking compared to before and that lovely little pocket of fat between a tank top and my underarms is suddenly back (again, no weight gain). I like the concept of New Rules. Lifting weights is my true passion. I love the set-up: full body workout on a 2 day split with compound moves. I like the way it alternates moves, like your push-ups and your rows.

Here's the part I have a problem with. If I continue NROL4W, I'm not progressing towards my ultimate goals of squatting and deadlifting my body weight. How could I? There are no more basic weighted squats. They vary each phase now. Same with deadlifts. I want to go heavier, not deadlift off a box or whatever variation. I need a better, more challenging routine set up the same way but also including isolation moves. Anyone have any good routines to suggest? Or has anyone finished the whole 6 months of routines and turned out completely happy with it? Or has anyone altered NROL4W by supplementing and adding in different moves and kept going with it that way?