I agree with the last two posters:
Try moving the shoulder straps away from your neck a little and toward the ball of your shoulder. Try different placements, if you haven't already, to see if some specific spot is golden and the pain goes away!
And crossing the straps over your baby before tying is a good idea too. Trying different things like this is the best way to find out how YOU are going to be comfortable!
Here's my instructions page for a front carry (sorry some pics aren't working--it's under construction): http://www.wrapyourbaby.com/meitaifront.htm
Steps 6 and 7 show two different ways to try tying the shoulder straps and you'll just have to image step 8 (it's what pp posted a picture of, I believe).
And my back carry instructions show some similar options in the back carry (in retrospect, black straps on black t-shirt: not a great idea): http://www.wrapyourbaby.com/meitaiback.htm
Regarding the waist straps being too tight, have you tried tying them on a little looser? Too obvious? As long as it doesn't interfere with how close and high your baby is on you, it would be fine. They shouldn't be constrictive! If you do end up altering your MT, maybe a little padding in the waist straps would keep them lying flat and broad around your waist, and not turning into a tight rope, if that's what's happening? I'm not a sewer
I think your pics look great, actually. Nice positioning all around. I even think those little knees look fine--the legs aren't dangling and the baby's weight isn't all on the base of her spine. It looks to me like his weight is on her bottom and thighs. As her legs get longer, the knees above bottom look gets more distinct.
It's just a matter of tweaking it to your comfort. It would be nice if you could do that by adjusting your method, but it could also just be that they need padding!