you hav the wrong valley cover bolts bro..the ls6 valley cover uses low profile allen key bolts. if you didnt notice your bolts are slightly higher then the steam lines.

 

The valley cover doesn't even play a roll in the situation. The coolant tubes are in the same position regardless of what valley cover is used and as illustrated time and time again on these boards, the LS6 manifold fits perfectly fine with the LS1 lines.

As Johnny pointed out, the bolt heads my protrude higher than the lines but judging from the picture I see no reason why it wouldn't work.

 

Thats only if you have a fast intake.... I agree the op needs to either get the ls6 lines or hammer the ls1 ones. People get all hung up about ls1 crossovers but gm has used the ls6 style with blockoffs on literally every car made after 03 so I think theyre good lol

 

That's what I say, people really over think the coolant flow "issue" with the ls6 lines. The only time you need the lower profile bolts is if you're running the FAST intake. That has nothing to do with the issue. The only issue he has is that the coolant lines are laying on top of the dimples that the PCV and oil separator on the bottom screw into. His 2 options are to heat up the ls1 lines and bend them around the dimples to lay flat or go buy the ls6 coolant lines with the blockoffs. Either way will work and be fine.