Rogue Atlas Magnum sounds bright -- any recommendations?

I hear you on the input tubes and have some nice NOS 12au7 and 12ax7 tubes to roll through the amp. I have Cerious Technology GE IC’s in my rig so I will live with them.

The GE ICs are very detailed and revealing so chose your tubes wisely. Your small signal tubes should not have extended highs.
It looks like the 12AX7s are in the gain stage and will have the most influence on sonics. Mullard CV4004 or the longplate square getter should be on your list to roll, they’ll take the edge off. Brimar CV4004 is also a good choice, more dynamic than the Mullard.
Then try a neutral 12AU7 which looks to be the driver/phase inverter.

As others have recommended, change out the KT90s. Don Sachs uses KT88s, a good choice. The GL KT77s are a wonderful linear variant of the EL34.

I wouldn’t recommend going on the merry go round of swapping cables, stay with tube rolling.
What brand of input tubes do have on hand?

Lowrider,
I have a ton of tubes with poor markings on them so I gotta get them all to my  tube tech to ID them properly and test them.  I did swap some Mullard NOS 12AX7's in the amp and they seems to take the brightness down a fair bit.  The NOS GE 5752 tubes might also help.  

You are right to suggest swapping the KT90's out for KT88's or KT120, both of which I can borrow from pal.  They are all compatible with the amp.  I forget that the curse and blessing of tube amps is rolling tubes.  The NOS tubes are pricey.  Thanks for the help, my friend.  

Whitestix
 You would also have nice surprise you can update to Magnum II status
  Rogue Audio is in PA and if you are anywhere near they can bring that amp up to a beast level for very reasonable.
 The Atlas Mag II driving Vandersteen 3A Sigs Lou Reed and his fender on Animal Serenade live infuses a major smile and wow on everyone's face when listening.
      Best JohnnyR

JohnnyR,
Thanks for the encouragement.  I have talked to Rogue about an upgrade, which is affordable, but my experience with upgrading a boatload of audio gear, is that they pretty much just works around the edges and one can't get a nickel out the costs of the upgrade in the aftermarket.  I am gonna roll some KT88's and KT120 through it see if it sorts out the HF sibilance I am hearing.  The amp does a hell of a lot, but the hard edge of vocals is a show-stopper for my ears.  Cheers. 

I had Rogue Apollo monoblocks from 2010 that shipped with an all Electro-Harmonix tube complement - KT90, 12AX7 (gold pins), and 12AU7 (gold pins). That was indeed a very bright sounding complement. Almost ANY other tube choices you can make will be notably less bright; you don’t even necessarily have to go into NOS (though a few NOS tubes can be very bright, too). Start with Tung-Sol KT120 in place of the EL90. If you have Electro-Harmonix small tube, get rid of those too - e.g. maybe Mullard and/or Gold Lion reissues? I’ve also tried the Mullard EL34 reissues in a different amp, and liked those too. And a NOS short-plate Mullard 12AX7 will REALLY warm things up - in fact, too much IMO.