Hopefully tightening everything up helps.
As far as valve cover gaskets on the 3.4, they suggest to get new gaskets for the intake manifold since you may need to remove it to get to the driver's side gasket. Brad said he didn't have to, but he couldn't remember if that was before or after the supercharger was put on. :flipoff4: I did the passenger's side first since it was easier. Just removed the intake, unhooked the coil packs/wires, and cleaned the throttle body out while I was at it. I never took the time or effort to change the driver's side because I'm too lazy.
Also, when/if you do change the valve cover seals, get some of the black goo Toyota sells to put on the corners where it meets up with the hump for the cam. I just used high temp RTV since that's what I had.
Edit: My fan is really loud for a few minutes after first start up. It always has been, so it should be normal.