OK, I think the added length is going to help. You may need a bit of getting used to it. On Skagit you want somewhere in the neighborhood of 3X the length of the rod. You've got 39' with 12.5x3 = 37.5. You are right in there. How do you think you are getting hit on the bottom hand side with the fly? What path is it making and where does it start from? Also, why only 4' of leader? I never go shorter than my rod even when I add a sink tip.
One more thought. If you sweep your rod low coming into the start position and keep it low for way to long, essentially starting the cast with the rod tip way to low, you could swing the D loop back to your left behind you. That would cause the line to pass over your left side. If the fly was properly placed I think you would just hang your self up in the head, but combined with a blown anchor it would bring the fly crossing your back and over your left shoulder at a path aiming to your rod tip on your right, making your head a pretty easy target. It also takes a lot of power out of your cast dropping the rod tip low going into the start position. This would cost you distance. Trying to get that distance back by hitting it harder will cause the blown anchors.
You need to sweep low and steady coming into forming your D loop so that your fly is forward and right of you. There should not really be a pause because you should be doing a sustained anchor cast. Come up into the start position with the rod tip high and without a real pause (watch your head and fly placement though and make sure you have the fly in the right position and the anchor ) and go into the cast. You need to stop the rod tip high on the end of the forward stroke also. Going to far forward with that short a head.
Also, that trying to speed up was I am sure part of the problem. Where does your fly hit when you do the snap? You may want to aim it for farther up river and farther out. I think your placement is part of it.