are the injector connectors the same? not a big deal if the are, but something to find out.
LS6 is a 24x reluctor, something I found out earlier when I was killing time during this fine little xmas vacation, so you're good on that.
yah, I would just do what Frenchy said and get a truck harness and flash the 0411 PCM for the LS6. Since you'll be getting an aftermarket tune, the differences between LS6 and LQ4/LM7 stuff (not sure if they use the same MAF Hz table, spark tables, VE, etc) in the tune should be taken care of. What kind of trans?