I had the same problem also. I've got a 3.5" rox pivoting riser with stock windshield and Madd handguards.
I am still using factory cover, but I have linchpins for the handguards. The mount stays on the sled and the guards come right off. During trailering, I put the guards in the trunk. The cover is a tight fit, but still works good.
On a side note: the guards have a little play(and I mean little) with the pin, but I'll take the play over having to mess with removing the small *** mounting bolts all the time. I found the largest pin that would fit in the holes.
Hope this helps.