Focal Aria sounds muffled and far away being run on a denon AVR-X3400H

First, we need to find out if it is  your speakers or your room.

Assuming you have connected them to the correct amp posts, the next thing is, set the speakers about 4 feet apart and put your chair 4' from them. Do they sound a lot better than far away?
That difference is room acoustics.

If they still sound muffled, it's your electronics.

One thing to be aware of is Focal is kind of a devotee of low impedance right in the "punch" area of the bass. I haven't seen a complete impedance curve, but with those mulitple woofers, and a 2.9 minimum impedance it is safe to say this could be an issue.

If the issue is room acoustics, or placement, then I recommend GIK acoustics. It is always a good place to start no matter what.

This would be primarily for home theater use with ocassional music from streaming and vinyl

I have made sure they are connected to the binding post correctly. Also they sound the same no matter where I am

Then it's definitely the amp. :(

One thing, if you have room correction, turn it off first. :)