I'd...

....have all of my plumbing enter the VF at the same location so I could peel
the liner back to re-work the hole. Right now, I have a pipe on one end and
on one side, so I can only peek it back so far.
....bury my plumbing much deeper and have it enter from the bottom of the
pond, so I could then have it go as high as I want, or keep it low.
....be careful not to contaminate my water with the surrounding clay as I
worked around the lined hole.
....spend more time working wrinkles, folds, etc. out of my liner.
....consider how hard it will be to work on the pond, with a 1/3 of it is
under a bunch of pine trees.
....I'd create more shelves at different depths, and make them totally flat
instead of angled slightly towards the bottom drain. This would give me more
choices in plant placement, and make maintenance much easier.

Care to add to the list?

--
BenignVanilla
Pond Site: www.darofamily.com/jeff/links/mypond