Yeah, Chaosphere is where it's at for Meshuggah's best tone IMO.
In the meantime, when Gareth calms down, I'm gonna play a lot more nicely and give you advice in a way that will be condescending or insulting in any way.
To the OP, I want you to do this for me:
In your DAW, or whatever, insert a track from Pantera's Vulgar Display of Power which is basically one of the quintessential mid scooped tones.
And then next to it, place a track from Chaosphere, or the I EP or Bleed, whatever, but basically not anything from Nothing, because that was their worst tone/mix from the post DEI period anyway and I agree with Gareth on that.
You will hear a fuck ton more mids, less fix, far more clarity and articulation, and WAY more percussive chunk.
If you can re record your song on a longer scale instrument and with more mids, do it, because it'll sound infinitely better, I can guarantee.
The reason why Meshuggah sound like they do in their more recent times of using 8 strings is because :
A. They use 30 inch scale guitars which allows them to use a sensible string gauge that doesn't have terrible intonation and the longer scale lends itself to far more clarity and attack in those kind of depths of tuning.
B. They have the right kind of pickups for the pickups for the job. I don't know what you use, but I do know Meshuggah now use Lundgren. You might already be using EMGs, I couldn't see from the video, but those are also super good for maintaining clarity at lower tunings (EMG 81 in particular, for 6 strings anyhow).
C : The mids are prominent enough that they enhance the percussive nature of their playing, but not so much that they make it sound honky which in the case of any guitar tone is generally when you've added too many mids.
D: The guitars work with the bass guitar.
They compliment each other.
The key word is compliment here.
If you simply add a bass guitar to the current tone, you'll be supplementing it.
They wont be really working together, instead you're just trying to add bass guitar to a tone to make up for it's inherent weaknesses, which will only further damage the tone and make it worse.
Build a good guitar tone from the ground up and then sculpt the bass guitar around it.
It's going to be far easier to re record the guitar tone, get it good and be able to work the bass guitar into that, rather than recording bass and fighting unnecessarily to try to get it to glue together right.
Here is a good thread concerning bass guitar tone:
http://www.ultimatemetal.com/forum/production-tips/484245-metal-bass.html
Hope that helps.