I have the same Juki as yours, but I have not encountered your problem. Sounds frustrating!! To answer your questions, I use Gutermann 50wt cotton thread for piecing and quilting, and use the same thread on the top and the bobbin, but may vary the colors. My machine came with size 14 Organ needles so have stuck with the organ brand. But I did buy some size 16 titanium needles and really like them so they are what I use. I also stitch between 2.5 and 2.75--if I go above 3 in length my machine seems to gather the fabric a little and am going to have my dealer look at this when I take it in for annual cleaning. I use my walking foot a lot and it stitches fine but does make an intermittent clacking noise that drives me batty.