Not sure of which mounts you have but in order to put an LS engine into an OBS, it generally takes the 1" setback to the rear engine mounts in order for the transmission/crossmember to bolt back up in it's original position.
My engine/trans is also mounted 1" forward of where it should be due to having the wrong mounts. I haven't had any problems with the rear driveshaft although the front driveshaft was a little tight getting in. Already have 2500 miles on the swap and haven't had any problems with the shafts.
'93 Chevy 1500 4X4 ECLB with a '99 Silverado LQ4 6.0 and '99 Escalade 4L60E. SOLD IT!!
New toy: 2001 2500 HD 4X4 Extended Cab Long Bed
John