When we customized our first BMW’s we had a high mudguard ‘Midlife Crisis’ check it out here http://www.untitledmotorcycles.com/2010/09/finished.html  -  We didn’t have any issues with the mudguard hitting the tire as it was fixed to the rear subframe. For our 3rd BMW custom UM-3 Street we wanted an old british look to the bike so we had to have the rear mudguard really close to the tire. This can cause problems in two ways first the mudguard can rub on the tire if not positioned properly and 2nd the subframe could hit the mudguard when the rear shocks are compressed. It is a fine balance between aesthetics and a functional ride. It looks and works great as we have fine tuned it. The photos below show how we make our stays to hold the mudguard in place. Without the 4 of them the guard wobbles and looks like it will fall off after a few rides. With them it is sturdy and looks very authentic. 
I’m not going to go into major details of measurements describing how long to make each stay or where you bend the stay as your mudguard could be a different shape to ours and you might not be doing this to a BMW!!!
  1. Get some iron profile round tube we use 12mm in diameter  and 1mm thick. I buy 2m lengths so I have enough left over for other jobs on the bike or if I make a mistake I don’t need to go back to the shop for more. It cost £12 
  2. Cut the tube into the lengths you need to keep the guard away from the tire. I always cut them a bit longer than needed. I start with the 2 stays that are roughly in line with the rear shocks [see photo 8]. Great the height correct to allow the nuts and bolts not to rub against the tire that is very important. 
  3. Once you have cut the 2 front stays squash the ends flat in a vice or with a heavy hammer. Ensuring that both ends are on the same plain. [see photo 2]. 
  4. Once you have worked out your rough lengths you can bend the stay at one end to match the curve of the guard [see photo 4]. We attach the stay to the guard drill your hole in the guards first and then work out the correct length of the stay and drill the other ends [see photo 5 & 8]  
  5. To attach the bottom ends of the stays to the bike we make a small plate that bolts behind the shocks [see photo 6]
  6. Once the 2 shock stays are in place you can then cut and place the 2 rear stays using the same techniques as before [see photo 9 & 10]
  7. Once all 4 stays are in place check the rear tire does not rub on any parts. The stays are ready for paint or powder coating.
Hope this helps and if I have missed anything out or it doesn’t make sense please let me know.
Adam

Look at the swing arm to see the bracket welded on to hold the mudguard
photo 1

photo 2

photo 3

photo 4
photo 5
photo 6
photo 7
photo 8
photo 9
photo 10