How do you have the aluminum plate oriented? I was confused by that, and initially had it upside down and rotated 180 degrees from what I now think is the right way to have it. Having the groove on the U on the bottom vs the top would raise up the hot end some and possibly be your problem. If that's already right, I agree on cleaning out enough material to get the extruder base sitting flat on the carriage.

On my newly printed base, I had the opposite problem and added a few pieces of kapton tape on the top end of the hot end... I wonder how consistent the aluminum plates and hot ends are. My Hex hot end and aluminum plate don't fit together tight at all - I shim the channel with kapton tape to tighten things up.