Have you bothered with the speed control? I had the same problems you have with the Juki with a Brother 1500.
I do use the speed setting as my inner timing seems to change every time I sit down. I have the feed dogs down, but can still sense them moving as a hint about how fast or slow I'm going. I've successfully used clear poly for a whole quilt - not bragging about the actual quilting which was not as even as I'd like it, but got the needle threaded and the tension right so the machine just sewed.
If your bobbin and top thread aren't close in size - I grabbed a bobbin of embroidery bobbin thread with a heavy top thread just for decorative and it got messy.
I just had some fits with straight line quilting. Think I had King Tut or Superior on top, and a lighter thread on the bottom. The stitches were way off. I switched both to a fine poly and things got better.