I take my seat off when I clean my bike so mounting the rack under the seat just saves a little time of not having to remove the rear rack bolt, plus I like the look of the seat rack on top. The knurled nuts have plenty of threads to hold tight.

 

On the rear seat bolts makes the rack sit up to high off the fender for me. Bolted under the seat bracket on the front and directly to the fender(with rubber washer) on the rear makes the rack hug the fender and it sits the same height off the fender from front to rear. I know, to ****, but its in the DNA.

 

Did you ever get around to extending the seat studs? Advice please!

 

Extending the length of the seat studs is an easy fix. Remove the plate that holds the current studs. The studs are basically a press fit, so take the plate to your vice/anvil and just pop them out. Replace with bolts 1/4" longer than stock length and add a spot weld with your mig welder for good measures. Then drop a thin wire or string down through one of the plate mount holes, attach it to the plate and pull it up into place. Replace the plastic washers that hold it in place and vallah! your all set. I had the same issue when I added the Motherwell fender rack. Total fix time about 30-40 minutes. Good luck.