Yes engine off, draining the ps should get all of the fluid no need to short flush.
on the tranny front I use mobil one synthetic and have been very happy with it. This is up for debate though as I am sure there a few threads out there dicussing the various fluids one should use.
2005 320 CDI
2006.5 VW Jetta TDI
1991 560SEL (179000 Sold)
1972 280SEL 4.5 ('The Lead Sled' 320000 miles when sold.)
1972 220D (225000 when sold)