How to identify my weakest link?

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. 

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).