Hi Craig, like Lee says, in a pickup with the extra space, 'upright' is technically superior (mainly for oil flow reasons), and pretty much essential for any later TDI which can't take the JX sump. However going upright does involve major extra complexity/cost to the installation.
If (big if) the turbo oil flow issues can be cracked, going 55 degree with JX bits is the path of least resistance, and plenty of people are running round quite happily (myself included) with this setup. I only get very minor smokiness under normal conditions, acceptable to me anyway. I think use of the Passat manifold may have helped as it keeps the turbo higher compared with adapter based solutions, see
here, also careful design of the return pipe.
For my install, I followed the KISS principle, and kept everything pretty much in stock locations, except I moved the JX airbox upward to make space for the
chargecooler and pipework. There are some pics of this on my brickyard thread. I've got some more I didn't post, let me know and I can email them if you want.
HTH, Andy