Since you don't show a layout of the deck, one can only answer in
generalities.
Many levels & only 20 joists seem difficult to match.

(1) Place a beam along the changes in deck elevation. Frame the joists
into the beam using joist hangers or ledgers. As an example not
intended to be a structural solution place two 2x12 on edge at the
change in elevation. As it suits the arrangements, the top of the beam
can be set at the top of the upper or lower joist. If the upper joist
sits on the beam, a band board can be used to tie the joist ends
together and serve as finish.

(2) The masonry piers should be supported by and tied into continuous
footers. If you are near the water, you need to set the footers deep
enough to avoid undermining. If not, you need to set the footers on
undisturbed soil.
(3) Yo no intiendo jefe.

(4) Flashing must lap under the building paper or house wrap at its
upper edge. It should lap no less than 3 inches at a point 6 to 8
inches above the deck surface. It should then cover the ledger on which
the joists sit. A better approach for a low deck is to make the deck
independent of the house. Thus a 1/4 or 1/2 inch gap allows the house
wall as is.

(5) If the deck boards are set tight like a porch floor, sloping the
deck is helpful - mostly to insure that what is supposed to be dead
level doesn't happen to slope back against the house.

(5A) Setting the deck a half inch below any door threshold is critical.
This keeps wind blown rain partially away from the door threshold
assembly.

(5B) There really ought to be pan flashing below the threshold to keep
water out of the house floor and floor frame.

(6) Give the tree room to grow. Set piers and footings to cut as few
roots as possible.