Separate playbacks for vinyl, cd?

"Through research and experience, it is my opinion that the components heirarchy in respective medias is different enough as to justify investing in two systems. Analog being focused on the source to output and digital having a greater emphasis on the amps and speakers."

I'm not sure how you came up with all that. There's absolutely no reason have 2 systems. Its much better to have one really good one.

"Another driving factor in this curiosity is the signal gain, vinyl being soo low and digital being soo hot."

That's not an issue. That's what the phono preamp is for.

Yes, vinyl needs a tube path and that might lead you to change speakers that are more sensitive to tubes.

First, I echo what Zd542 said. Assuming proper diligence by the buyer, two $1 components will never sound as good as one $2 component. The very concept is, pardon me, irrational.

In 35 years of buying, selling, setting up, adjusting, reviewing and above all, enjoying audio components, I've never once heard an upgrade that didn't improve both analog AND digital sources. Any component switch which favors one over the other is not an upgrade, it's a lateral move from one flawed component to another, differently flawed component.

A better component is not one that colors certain sources to mask their inherent flaws (all sources have flaws). A better component is one that's more transparent, more revealing, less colored, more true to the signal that it's fed. If transparency reveals flaws in some source or other, be grateful that you've identified the next system problem to solve. You solve it by addressing the problem at its source, not by covering it up with flaws in other components.

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I'm thinking about a dedicated phono stage that has a good mc option into a good quality tube amp...

Excellent idea. A good quality tube amp (like a good quality amp of any type) will make ALL your sources sound better. Tubes are ultimately my preference too, but not just for analog sources. In this I disagree with Buconero. My tube preamp and amp sound fantastic with any source.

... upgrading all the cables and connectors for the vinyl

Good idea, but upgraded interconnects, speaker cables and power cords will benefit your digital too.

...and keeping the CJ and Mc

... if those are sonic problems with ANY source, you'd be better off selling them and using the proceeds to help fund better preamp and amp.

...and upgrading speakers that better suit digital.

I've heard hundreds of speakers. Never once have I heard one that "suited" digital more than analog, or vice-versa. To the extent that it's good, a good speaker will suit every source. To the extent that it's crap, a crap speaker will suit nothing.

With respect, I recommend rethinking your priorities before spending any money.