Unobtanium parts when I did mine;
PF wiring harness (obviously)
Metal bracket for 'Vault' red and green light plastic + wiring harness.
Plastic for 'Thing' ramp red and green light + wiring harness
Correct lower cabinet harness (there are some subtle differences because of the knocker position)
PF Light boards (especially the mansion one)
All ball guides (especially the large orbit that goes from top right over to mid left of the pf)
All wire ball guides (the little V shaped one up near the Thing scoop would be a bitch to make)
The lower part of the 'Thing' box base (last I checked)
Timber side rails and guides
P/f backboard
"Kick Bear on centre ramp.." ramp plastic metal brackets
bookcase opto sensor boards and also lenses
Wiring harness for bookcase assembly
Wiring harness for bookcase opto board's
Wiring harness for Thing hand
Wiring harness for main ramp assembly
Additional flipper driver board
Telephone plastic mounting brackets
Thing hand opto pcb

This is all off the top of my head to some extent, and looking over old scratch build photo's.
Its the little things that catch you out, just when you think you are getting close to having everything needed.

I finished my scratch build, machine looks fantastic. Would never do it again though...