John - I will bet $1 that stock tranny mount is cracked. Mine cracked after 500 miles...the part was made in India and very very flimsy (I also have the Olthoff Motor mounts...great investment). Could be a possible cause. I switched to the Poly Trans Mount sold by Cobra Valley...worth every penny. My pipes dont move at all.
http://performanceunlimited.com/cobr...ransmount.html
I believe you will have to jack the motor up some to get one header out.