Sounds like basis for a good system. My only concern would be #4 as that is the one that could result in running up some scores especially late in season when team realizes they need to kill some teams to lock up position (as I would assume the close power house teams will be getting the 3 pts most the time anyway) I would rather see a third game to decide if Head to Head was split, of course with the pt system chances might be less of getting to a #4 beyond head to head.
I would give shutout pts at only 1. That would score the 4-1 would be 6pts (3 win 3 GD) and the 1-0 would be 5 (3 win 1 goal 1 shutout) actually makes a 2-0 shutout equal to 4-1 win) max pts from a game (3-0) is 3 win 3 GD 1 shutout =7. Which is only one pt better than 10-1 win kind of make the shut out worth a little and the pain of losing the shut out late in game due to freely subing much less.
Yes TLH has had the luck in PK's the last two times so they may also want to avoid going for "third times the charm!". I have seen Alyssia play and yes she can be a game changer. Getting Clover instead of FM is not a winning situation for anyone just a different one. No free pass either way!