First let me say that your quilt is gorgeous!
As for fraying threads, this happened recently to me also. I have an older Viking, but it's always worked fine for me. My chosen thread, in the past, was Signature cotton in both top and bottom. This time I wanted to use Twist from Superior and I thought Bottom Line would be my best companion. If I wasn't shredding thread, I was getting those nests underneath, or skipping stitches. I have a drop in bobbin so didn't think I could adjust anything there. I did everything imaginable. Then,,, I took a day off and when I came back I replaced the needle again, rewound a bobbin on low speed and through the channels but not through the needle just under the pressure foot. I chose a different cone of Twist, a different spool of Bottom Line. Basically, I really started over. And,,,, every thing worked. Not positive to the real culprit, but, a thought,,, if you have been shredding thread or getting nests you could have minutely bent your needle, especially if it's skipping stitches. I'd start with changing out the needle again, not that expensive when you consider the work we expect of them. Also, our bobbin threads need to be wound through the channels for proper tension but not on fast speed, as that can actually warp your bobbin. And one other thing I did, that I have no idea if it even had an impact. On my drop in bobbin area, there's a screw on the right hand side. Looks like it just holds everything in place, but I turned it to the left a fourth of a turn.
Best of luck on your search to getting things humming along in your sewing room once again!
May God bless the work of your hands,
Luann