The only problem I have ever had with wheel pants are on smaller wheels, say 2-1/2" or smaller and flying off grass, The wheel pants tend to drag in the grass and either try to cause the plane to nose over or slow the plane down so that it either takes most of the runway to take off or I end up aborting the take off all together. In these cases I take the wheel pants off and fly without them.
By my calculations if I have 1-1/2" of exposed tire under under the wheel pants I am ok. anything less and forget it.