some clues to get the ball rolling...
piece 4
up(?):
I will let your door be spun (5)
pivot
I'm a letter, not the start, (5)
omega
I'm a smell that you should ban (4)
right(?):
I'm with ocean in part one (6)
I'm before you'd say in Rome (4)
Canoeic palindrome, alas, (5)
tanka, meaning = oceanic, anagram of (canoeic)
down(?):
I'm three less, if upside down (4)
five / nine (thanks @Penguino!)
I can swirl, flow, stick and foam (4)
And one of three who might be us (6)
myself
left(?):
I'm a distance you can run (7)
yardage/ furlong?
I am therefore from Descartes (4)
ergo
I pay taxes to no man (6)
piece 6, one way around:
Tight (4)
hard
Lincoln (3)
abe
Speeded (4)
sped
??? (word was smudged beyond recognition) (5)
Twinkle (4)
Panda (2) God (4)
?, zeus?
Twins (5)
piece 6, other way around:
Destroy (4)
ruin
Greenpeace (4)
ecol
Cupid (4)
love
Abbacy (7)
Superior (4)
only/ over
Circle (3) Thus (2)
?, so
Number (2)
no
A special hint (partial)
1st step:
decode it with rot 1 to get
The pirate's calmly waiting,
his legs still being bound:
How can he start, not knowing
What slithers in the ground.
Ymj psnlmy nx fqrtxy wjfid,
Xtrj qjyyjwx rnxxnsl - bjqq,
Ny sjajw rfyyjwji bmfy ymjd bjwj,
Gzy wfymjw bmjwj ymjd kjqq.
Rfc pmjjcp'q, rfmsef, gl nylga:
Fgq pfwkcq ucpc yjj gelmpcb:
Lmu fc gq apmqqcb: fc uylrcb
Umpbq rm em umpb zw umpb.