Trouble Decreasing Treble

My current setup:

VPI Prime Scout w/ JMW 9” arm
Hana SL MC Cart
Lehmannaudio Black Cube SE II
Line Magnetic 211ia
GoldenEar Triton 5

I recently bought the VPI and Hana to complete my setup (for now). Certain genres like electronic and indie rock (think James Blake and Sufjan Stevens) sound amazing while other artist with heavier rock influences like the Black Keys are frankly irritating to listen to.

As far as I can tell the VTA wheel on the Prime Scout is useless as it only raises the height of the cue lever and tail end of the arm. I’ve resorted to adjusting the VTA by lowering the pivot needle itself, but now I’ve bottomed out and while the bass is good the treble is still too high. Does anyone have any insight or additional info that might help me out?

Additional info:
Hana SL recommended impedance >400 ohms
BC SE II set to MC 1 kohm 

I’ve got,
Prime a Hana SL
Lehmann Black Cube se2.
Primaluna dialogue Premium integrated 
Focal 1008be2

I can tell you that setup is not bright, even with the Focals.

It’s extremely important to get the alignment on that cart as perfect as you can get. 
 I had originally set it up and thought it sounded great. However I ended up getting the Fozgometer and went through the whole setup again from the start. This time I was blown away, soundstage and bass was hugely improved. 

If you can either get a mint protractor, or print out one with really thin lines to align the cart it helps along with a really good magnifier. 
I use a usb microscope. 

Other than that, room treatments, speaker placement all contribute.

What turntable/cart did you have before?

Thanks for your response. I will look into possibly realigned the cartridge w/ a protractor as you suggested.

Prior to this I had a Uturn Orbit plus and an Ortofon OM 10 so this was a large step up with not a whole lot to compare it to.
To adjust the VTA on the JMW-9 arm you have to first loosen the two setscrews on the round base and then turn the adjustment wheel. Once the desired height is set you then snug up those two setscrews. This is briefly explained is section 7 on page 12 of the manual. By lowering the VTA you should effectively decrease high frequency output, as will lowering the load impedance of the phono stage. Hope this helps!
With great upgrade come great responsibility, I think Yoda said that.

You moved from a really good cartridge, to one that really needs special set up to get the best out of it. Shibatas are particularly finicky, but once you get it setup, it’s excellent. I moved from an Ortofon Bronze 2m and noticed a marked decrease in surface noise, better dynamics and soundstage. So stick with it!
I would first try "free" changes.  At 1k ohm, for the load impedance, you are running the cartridge a little "hot" in terms of treble response.  You could try a different loading, including a setting below the 400 ohm setting recommended by the cartridge manufacturer.  I would try something around 100 ohms, if that is possible.

If the cartridge sounds right with some music, but, not others, you will probably just have to live with some compromise setup.  

''The increased treble'' is well known problem by MC carts. I own

Klyne 7 PX3.5 Phono amp with ''High Frequency Contour'' by

which one can decrease HF by choice. The values between

15 Khz till 40 Khz can be chosen while the needed switches

are marked in the user manual. There is a list with 25 '''well

known carts'' with recommended values. I have no idea if other

phono-pres have similar provision. My other phono-pre; the

Basis Exclusive lacks such provision.

Too high a resistance load will make the highs rather piercing, get it too low and the bass goes rather too soft. It looks like there's provision to customise the load so you should be able to land right on the optimum with a bit of effort.How are you measuring VTF, If not at playing height are you allowing for the C fo G moving forward as the stylus is lifted? This will give a higher reading on your scales than is applied to the stylus when playing if your scales are higher than the record's surface. I used to use a Naim Aro uni pivot and for a DV17d2 it sounded it's best with a reading of 2.42g with the scales placed on the platter, with my previous Rega the playing weight optimised at 1.95g for the same cartridge (with the spring dialed out)