It's probably normal for things to feel stiff/uncomfortable/inflexible if you've been sedentary for a while instead of doing things that require you to move through long ranges of motion. Just try to keep stretching, moving around, experimenting, and it may get better over time.
But for some specific advice about holding the bar, here are some pointers to keep in mind:
1. The bar should start at mid-sternum in the rack, you might want to try using one notch lower. The act of ducking down to get under the bar seems to be useful to help get it into the right spot.
2. The wrists need to be kept straight when you place your hands on the bar before ducking under. The elbows should not be raised at this point - the arms should point back and down at a 45 degree angle.
3. When you duck under, you should come up under the bar at a 45 degree angle upwards. Imagine heading a soccerball up the field. You need to jab the head and torso up through this angle to force the bar to wedge into the right spot, you'll have difficulty getting it there without this.
Here, watch this video at 0:40 to see these 3 things in action, so you'll have a good idea of what to look for.
About finding the spot under your scapular spine, when you are getting the bar on your back, by putting it higher or lower you will feel it run over the bone, you cannot miss it - bar on bone is very uncomfortable. So put the bar on that bone, and then push yourself up a bit more under the bar, so that the bar wedges down past the bone and into your delts.
You deal with this by removing weight from the bar. Try 135 for starters, you should be able to easily squat ass to grass (and what feels like ass to grass for you might end up being the correct depth, who knows until you try)."I don't think I'm going low enough, how do I go lower without getting stuck at the bottom? It's only 215lbs can you believe I struggle with it!
Another thing to fix: notice at the bottom of your squat how your lower legs are way outside of the line of your femurs. This means your stance is a little too wide. What you want to aim for is to have your feet, shins, and thighs all aligned in the same vertical plane.