Hi Craig,
Did you split the cable at the join or unbolt it from the gearbox casing? If you split it then it will go back properly regardless of where the box or the shifter are now.
If you unbolted it from the gearbox then you may need to re-adjust the shifter to suit the box as the bracket has about 4-6mm of adjustment if memory serves. If you leave the two bolts slightly loose when you put it all back together then the shifter will pretty much find its own centre so once the box is back in and the cable reconnected just nip up the two bolts and then check the shifter is selecting the right gears with VCDS. Should be fairly simple
Regards,
MJ