Regardless of which mounts are used, they must be the 1" setback type. I also ran into this issue with my 6.0 swap into my '93 4X4. I used plates that put the engine into "standard position". To me, that meant in the right place, not 1" forward of where it should have been. I also had to slot the holes in the cross member to get the trans to land on it. The rear driveshaft still fit, but the front driveshaft was now closer to the front axle by 1" and needed a slight trimming to fit. I don't have a shift cable, just the old style linkage. That too had to be modded to fit the new location.
Not sure how you could proceed. Any way of detaching the cable and pulling all slack out of it to make up the 1" difference? If not, maybe jack up the engine and replace the mounts with 1" setback types.
'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