PCI-E Gen 3 will have very nearly zero effect on the score.
Please also look at these scores:
http://hwbot.org/submission/2377088_alibabar_3dmark_vantage___performance_geforce_gtx_560_ti_448_31607_marks
Only 180 points behind you, with over 200MHz less! on the core and 75MHz less on the GDDR....(not even using drivers that allow >1GHz core)
This one: http://hwbot.org/submission/2258875_rkinslo_3dmark_vantage___performance_geforce_gtx_560_ti_448_30375_marks
Comparing is a little more difficult because of the CPU speed but look at the GPU MHz. You have a 30% advantage in core speed and15% in GDDR clocks, but only 10% higher GPU score. This score does not have LOD either.
http://hwbot.org/submission/2253233_cowgut_3dmark_vantage___performance_geforce_gtx_560_ti_448_30236_marks
Same here. You have 20% higher core, almost 10% higher GDDR. 350MHz more on the CPU.... and only a small increase in GPU score. Again, this score has no LOD.
I can keep going bro. Your efficiency is off.