How to identify my weakest link?

definitely cartridge and small signal tubes on the rogue.  

cartridge upgrades would include an audio technica AT ART9XI and better still a Lyra Delos.  Both are amazing and excellent values at their price.  

as for tubes i had a cm ii and loved it.  tried dozens of NOS tubes and the best ones really make a difference.   tried them all including brimar, mullard, rca, ge, mazda, philipps, amperex, gold lions, tung sol, jj, sovtek, telefunken, sylvania and others.

i could not improve on the exquisite sound of amperex holland or made by amperex 12AX7s and 12AU7 preamp tube. amazing.  For the pair of 12AU7 you can take your pick from the stock JJ, RCA 5693 or 5814.  an investment yes but also solid upgrades. 

If you love your speakers, then cartridge is looking like your easiest upgrade here. A sub-$1,000 MC should be significantly beaten by most $2K+ MCs or MIs. You already have way more than enough phono stage and table to handle a large upgrade. I just wouldn't put say a Koetsu (heavy and low compliance) on that light Magnify arm, though. 

Also agree with @avanti1960 - NOS small tube rolling in the Rogue will reap solid benefits. At some point you'd also want to look at either separates, or a more upscale integrated (like VAC). But the Cronus should be fine for now. 

Trying another cable brand could reap dividends too (current Synergistic Research and Audioquest lines are nice), but that's possibly more hit or miss than the others. 

@avanti1960 yeah I looked at the Lyra carts. From what I’ve read, I might be better off with something a little less analytical given the speakers I’m running. 
 

@mulveling Thanks for the ideas. I think I’ll start with cables until I can decide on a cart direction. I’ve also thought about going the Clearaudio Concerto MC given I’m already running the Ovation. So many options. 

The Benz cartridges are very musical, with a touch of sweetness and warmth - not at all analytical. They’re excellent for the money especially if you peruse the FS ads here. Any of their "L" (low output) models in a Zebrawood or Ebony body are pretty stellar. And a piece of cake for your Herron to amplify (well except for the Ebony TR but that thing’s crazy). Could be a great sonic match with your table, amp, and phono stage (and possibly speakers) all falling on the clean-neutral side of things. Rogue tube amps are certainly not warm nor "tubey" sounding. I don't expect any difficulties for the Benz in your Magnify arm, either (which is an arm I kind of like - what I hated was the all-magnetic Clarify). 

Nice system Paul! I think your inclination to look at different speakers and, if necessary, a complimentary amp is spot on. It sounds like you have some issues with the speakers that are beyond the ability of tweaks to address. Personally, I’m not a fan of B&Ws—you can do better without spending a ton of money and probably find something that works well with your integrated. Generate a shortlist and take your amp to a few dealers to see whether something else tickles your fancy. Good luck!