I looked in an old issue of Performance VW i have - theres a great example of an older Passat with a VR6. The engine bay is just perfect.
Theres also a mk.2 Golf which has also been cleaned. Sorry i've been searching for 15 mins now and I can't find anything at all.
Basically the most you can do seems to be removing the wiring loom, lengthening it and routing it through the chassis legs. Also I suppose you could remove the secondary air pump and plug it up. smooth and paint the engine covers and battery cover? or relocating the battery to the boot would be easy, but underneath the battery is not pretty ...
anyway if you want the issue i have is PVW issue 10, 2005.