I would be curious to what port on the intake that the hose is running to that valve cover. It should not be going to the intake manifold. If you are running a hose from the 1/2" hose on the back of the intake to the drivers valve cover rear port, this can be a big issue if it does not have some kind of PCV valve in that line.
Here is how the hoses should be run on a stock LS1 engine, regardless of an LS1 or LS6 intake.
The rear of the drivers valve cover crosses the back of the engine and "Y"s with the rear of rear port of the passenger valve cover into a single line and then to the PCV valve. Then from the valve it runs into the port at the front of the intake on the passenger side just behind the throttle body. This makes up the vacuum side of the PCV system.
The port on the front of the passenger valve cover goes to the port on the throttle body on the passenger side near the throttle stop. This is the fresh air or breather hose.
On the back of the intake, the large hose (1/2") is your vacuum line for a brake boost. Since you have manual brakes, this port should be blocked. There is also a small port (1/8"?) that is normally used for vacuum access for the AC or other accessories. This can also be plugged off if need be.
That is is as far as "normal" goes.
With not being able to see what you have going on with the passenger side valve cover ports, I am hard pressed to tell you what you need to do, but here are a couple ideas based on the above "normal" setup.
You can eliminate the drives port by plugging it off and just running a single hose from the passenger valve cover rear port to the PCV valve and then to the port at the front passenger side of the intake just behind the throttle body and then keep the breather hose as "normal".
You can again eliminate the drivers valve cover port by plugging it off and then running a new PCV hose from the rear of the passenger valve cover to the 1/2" vaccum port at the rear of the intake, but you WILL NEED to add a PCV valve to this line to make it work properly. If you do this then you can again run the breather hose as "normal".
Now if you do have it setup as I am thinking from the first paragraph with no PCV valve and had it custom tuned this way, it will have to be retuned if you go and set it up the "normal" and proper way. This is due to the rate of change in how much air will be traveling through the PCV system.
Hope this helps.
Mike Norris
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