Can't tell from your pictures if the brackets are swapped. The engines have a tilt to them with proper installation. If the brackets are swapped I think that it does bring the left side up, making the top of the valve cover more level. It can look correct but be wrong. The simplest way to tell might be to check the bottom of the oil pan. It should be level from left to right.
Hate to say it and maybe, subconsciously, you already know it but it looks like that custom intake manifold could also be the problem. Where did it come from?
Good luck.