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Dark Tone

If I understand what you mean by 'dark' but not 'mellow', I would tend toward a good EQ pedal, probably an Empress like GretschBassist said. To me, mutes and flatwounds definitely 'vintage up' a tone, and may introduce other things you don't like along with the darkness. I would probably also tend towards a series-wired bass; a precision will work, obviously, but a jazz in series or something with series soapbars also would, and maybe give you a bit more definition. A cab that can go big down low also important.
 
Dark but not mellow?

Sounds like you want a short scale.

Wait, I see in your signature you already have a SS Jag. What kind of strings are you using?

In my mind you've got to be at least close to what you are looking for already with that bass.
 
Listening to the clip you posted, I'd say that sounds a lot like Jimmy Haslip's tone. There are a lot of low mids in that tone...maybe boosted around 400-500 Hz? So, do that and roll of your passive tone knob to taste.