All the problems described above sound like they could be tension related. Are you free motion quilting or are you doing walking foot quilting?
You can get bad threadnests on the back of a quilt when fmqing if you forget to put the presser foot down because the tension discs do not engage unless the presser foot is down.
If if you are not fmqing, and your presser foot is down as it should be, then the thread nests could be a result of too loose a tension on the top, or a mis-threading.
The section where your top thread was laying along the surface and pulled out like a feed bag string sounds like too tight a tension on the top thread. Which is the opposite problem from the bird nests. Did you maybe loosen the tension after you'd quilted the first part?
Rob