For the rat's nest (I called them bird's nests) I'll only say. Stop threading the needle with the presser foot down. Trust me. That's the trigger that causes the nest underneath. FWIW, That's not bobbin thread. it comes from the spool.
The other issue is If you are using basting tape. You need to clean the needle regularly with Goo Gone or Sew-Eeze.. I clean my machine every bobbin. And My machine is nowhere near heavy duty.
Lastly only bonded thread. the fuzzy stuff catches the gummy way too easily and that causes the majority of your missed stitches.. Avoid cotton thread. Use 100% Poly Bonded thread. (I like size V30.) I you are making something big, Consider V46.