I'm not sure I recommend the back bay marshes of the nueces river. The paddle there is long and it's really easy to get turned around without a GPS or a good aerial map. The mouth could be an option, but you'd still have a decent paddle to the marshes.
I've spent a lot of time at Shamrock. It's good area with numerous flats of varying depth and channels to work over. I can count on one hand the number of tailing reds I've seen there, so you're more than likely going to be blind casting or drifting the flats looking for reds. Plus, there's lots of islands offering wind blocks.
BIB/PINS, basically has three ways to fish it. You can just wade the drop off (pretty obvious on google earth) where it goes from knee deep to 4 feetish. or you can set up with the wind and drift the deeper stuff. Either of those first two choices you'll want to concentrate of casting to the numerous sand potholes. The third option is to work the islands in between them where the wind generates current.
LHL and B&R are probably the two most popular spots in the area. I've had better luck fishing LHL and IMO gives you the better shots at tailing reds due to its shallower flats. It can be difficult to navigate especially since it has lost navigation markers since the hurricane (TPWD has a downloadable map: CLICK
), but it's not too bad. B&R offers decent protection from SE winds if you launch on the southside and use Harbor Island as a wind block. Both spots have spots to work drains/guts into deeper waters.
When launching foe Estes you'll paddle onto numerous spoil banks with guts draining into the ICW. There's a chain of back lakes on Talley Island, but I've never seen anything other than mullet back there. I'd paddle straight across to Traylor Island and work the Estes side of the islands or one of the three cuts out to the main bay.
As far as fly selection I'd keep it relatively simple:
Clouser in Chartreuse/White, Pink/White, and Grey/White
Small Popper in either White or Bone
Spoon Fly in Glow and Gold
Kwan in natural tan and pink
Shrimp Gurgler in natural
During warmer months I'd add a crab imitation as well
I pretty much just use WF floating line, but if you plan on fishing more of the guts/drains into the channels a slow sinking line would be beneficial.