Trying to make the stuff I have work a little better.  I'm using a MacBook, a Focusrite Scarlett 2i2 or a Scarlett 18i8, and a pair of JBL305P MkII professional monitor speakers for tunes in my vault room .

Music sounds a bit muffled and just not quite right. What can I do to make what I have sound better?

Have you tried eqmac?

You can run REW to see where the room needs help.

Playing with that app now. Thanks! It does seem to help. Rocking out to the dead daisies rn.

Without running REW (Room EQ Wizard) you are relying on one of the most inconsistent measuring devices on the planet - your ears.  A good calibrated mic and REW will tell you where to start.  From there, choose the appropriate software that will allow you to create a virtual parametric EQ.

So right.

The easiest way is to set the room up right with the correct wall-wall-ceiling ratios, taking care of any surface issues, and then click start.

Audio receivers with audio calibration capabilities are incredibly cheap and very accurate as are the ones running on phones/tablets.  

When the computer is done I'll still run pink noise and use an audio spectrum analyzer program to see the results.

Using the software parametric equalizer filters in the subwoofers I dial those beasts in.

It used to take me hours using a calculator to run the first three or four nodes in a new room and then using an equalizer zero out each channel.

Did the sound ever sound unmuffled or is this a recent issue?

I would recommend checking your signal path and make certain there are no "enhancements" made to manage the sound. So nothing like sound leveling to make songs sound the same volume or enhancements for clearer sound or to sound like a certain club or concert.  You'll need to check the software playing the tracks, the speakers and any other items in your signal path chain. Also no internal equalizers or bass enhancements or mod enhancements. Get everything to run with as few of the enhancements a s possible, then you can tweak things from there.

Also, what quality tracks are being played? Are they MP3s, FLAC, WAV and what is the resolution of the tracks.  The better the equipment you have, the better the signals that should be fed to them.

As others have mentioned you can get relatively inexpensive but good quality receivers that have built in room equalization that is applied based on measurements to the listening position often with an included microphone for the receiver.

I've got he same audio interface and JBL monitors on my desk setup.

You say "vault room", I'll assume you've got some strange room nodes going on. Because hardware wise, that's some good stuff, and shouldn't sound bad.