While I agree with all the advice about cleaning I do have a question about thread. Since you used two different colors of thread it can't be that particular spool. So, the next thought, how old is the thread? Are both spools the same brand? Are you using the same thread on top and bottom? Are you using serger thread instead of sewing thread? Are you using a coated thread like hand quilting thread by mistake?
Thread can play an important part of your quality of stitches. If all else comes back been there, done that, then I'd be looking at the fabric you said is 'stiff' and/or batting that has lots of imperfections.
Hope you figure it out before your next project!