Sounds like a great trip with lots of options! Here are a few thoughts...

While staying at the Sugar Mill, definitely spend some time at Cane Garden (just avoid day if/when cruise ships bring folks). Also, hit Smugglers Cove.

From Saba Rock, consider having them drop you at Leverick Bay Resort and rent a car for the day. You can easily do the Baths, see Savanah Bay, eat at Coco Maya (although, I don't think they are open for lunch now, so maybe SugarCane in Nail Bay), and have an afternoon drink at Hog Heaven for spectacular view (must do), then make it back to Saba Rock for sunset and dinner.

Definitely go to Cow Wreck if you do Anegada, then check out the new bar next door, Tipsy's. You can also hit the other side of the island and do Big Bamboo and Flash of Beauty. Decent snorkeling there is calm conditions. If you want to do both, rent a car or Moke (at Anegada Beach Hotel), otherwise, just taxi.

From Scrub, plan a day trip to Jost - I would spend most of the day at White Bay (Soggy Dollar, Hendo's, etc.), and then a little time in Great Harbour to see Foxy's, etc. Also, maybe a day trip to Cooper Island and Norman (Willy T, snorkel Indians and Caves, eat at Pirates Bight).

Scrub Island has an hourly complementary ferry, so you can easily get to Trellis Bay (~5 min ride) and there are a few restaurants to choose from there.

I am not familiar with day charters, so no specific recommendations there. But part of the beauty and uniqueness of the BVI is to see all of the different Islands, so I think you are smart to get a couple of day trips (which won't be cheap).