I'm of the opinion that the left side is OK, but the right side hasn't warmed up yet. You can check the valves, but I would be surprised if that is the issue.
While the left side always gets slightly less air flow, the side-to-side difference isn't all THAT great, so I can't explain the difference. Air/fuel mix going through the manifold will tend to cool it, but they should cool equally, more-or-less so, again, I can't explain the difference. The manifolds get their heat directly from the heads.....Are the head/manifold gaskets the same thickness?
Drive it for 30-60 minutes and then do a touch test to see if they equalize. If they don't (one side is still noticeably hotter) then we can all provide a myriad of ideas for things to fix.