I had the same problem with my 3" DP.
It hit on the frame and header, and yes it
was a worn out motor mount, in fact you
can see that these motors usually lean a
little to the left with the stock mounts. The
passenger side mount always gets squished
down from the engine twisting that direction.
I installed the new polymounts from HRpartsnstuff
and now I have a 1/4 inch of clearance all the way
around my DP. plus it leveled my motor up real nice.
If you don't want to go to the trouble or expense of
changing both mounts you can just replace the
passenger side.