Okay this is going to be hard to explain and probably not going to make much sense but here goes...
1st - Open the hood and disconnect the prop mechanism either at the hood or from the engine bay.
2nd - Raise the hood up high enough that it begins to lift out - you may need two people for this.
You'll see that the hood pivots in the hinge on a black slotted (plastic?) piece, one on each hinge.
With the hood off, note the position of the black slotted plastic pieces and lift them out of the hinge.
You'll see that the slot isn't in the center of the plastic piece, rather it's offset to one side.
Turn the plastic pieces over and replace in the hinge, then replace the hood making sure it goes back into the slot of the plastic piece.
Then carefully close the hood. It should have raised the resting position of the hood from the rear allowing for the added height of the wingtop protectors.
Either that or it's made the problem worse,
meaning that the plastic pieces were already in the "high" mode.
Anyway, this worked for me in my previous D90. Yours may be different.