The drive shaft should have a mark to line of the flanges usually yellow or white. It can make a difference if its not lined up correctly as it is balanced. This can be checked though. I wouldnt be to concerned about it unless you can feel some vibration while driving in gear.
The egr bolts are 10mm bolts.
You dont have to hack up th eharness to relocate the PTU.
" I told my son, you have to catch the football other wise this just looks like child abuse." - My brother