Good Stuff, everyone. Couple more things. First, keep in mind that when you start doing serious workouts, some degree of DOMS is normal for perhaps the first month, but it should not be incapacitating. On the other hand, if you felt nothing whatsoever, you probably would not be doing much of an effective workout.
As far as warmups and stretching go, I assume, or hope, since you have a trainer, you are being properly warmed up. BUT... there has been absolutely NO scientific proof that PRE workout stretching prevents injuries or soreness. In some cases, stretching while the muscle is cold can lead to injuries.
As I've said many times, many women are hyper flexible, and pre workout stretching can actually be pretty deadly, in some cases. POST workout stretch is much more effective.
As far as your training regimen goes, you say you are doing 2 days upper body, 2 lower. On the days that you do upper, maybe use a different cardio machine than the elliptical, that does already have some upper body action. You can also use less resistance on the cardio machines, and work for more speed on the days that your muscles feel sore.
Another thing you can try, is playing around with your workout split. Sometimes, doing all upper body on one day puts way too much stress on the trapezius. There are a gazillion ways to vary the muscle routines. Your trainer can help you on that.
As far as your trainer goes, here comes a touchy subject. RANT WARNING...
I find it astonishing to see how many trainers have no clue as to muscle sequencing. Basically, you have your large muscle groups such as deltoids, chest and back, and your smaller muscles such as biceps and triceps. On many people, triceps are the weakest muscle in the upper body. But both the triceps and biceps act as assisters in performing chest, back and shoulder exercises.
I am always amazed when I see a trainer totally fatigue their clients tricep's, then ask them to perform something such as an overhead press!
So its really important to work the smaller muscle groups last!
As far as the other muscles hurting more than your injured leg, this is normal. They may be working over time to protect the injury. Also, the rehab you did probably did in fact make that area quite strong.
One more thought. If you find you are dissatisfied with your trainer, many physical therapists also do fitness training. I recall that your PT attended the Perform Better Workshops, so he does in fact have a knowledge of functional sports conditioning. You may want to find out if he can work with you.