Hi Bill,
Sounds like we have similar price pain-points. I stretched on the analog source and speakers, but $20K for a single amp/preamp component is well past my comfort zone.
I remember rolling a few times in the VAC Ren III preamp, and going back to the stock line-stage tubes every time! The one exception was the 1st 12AX7 in the phono section; I ended up with a super low-noise 1950's RCA in there -- not a huge improvement, but some. The only other way I found to improve upon the Ren III was a Bob's Devices 1131 SUT instead of the built-in Lundahls. THAT upgrade was well worth the money (i.e. just get the MM stage on this unit)!
My Apollos did indeed come with KT90; the KT120 wasn't out at that time. The upgrade to KT120 was significant, though that's the only time I've rolled the power section. Needing a dozen of anything (at least 6 matched pairs) just to try a new tube will definitely give you pause. The EH KT90 sounds a bit anemic in bass, dry in the midrange, and harsh/grainy on top compared to KT120. I.e. they sound thin in comparison. It's actually a decent tube, but doesn't stand up to the KT120. There were times when my system was in the transition throes of some other upgrade or downsize, and got a little too warm/mushy -- at these times, I'd try the KT90 again, and sometimes earnestly enjoy them again, though the re-marriage never lasted once I got the rest of the system back in line.
I didn't think to ask Rogue when I got my Apollos & Hera II (bought a Hera I used and had upgraded to II status by Rogue), but apparently they'll upgrade parts if you request it. I'd expect their fees/markup to be quite reasonable, as they always are. I'm definitely intrigued by the prospect of say Mundrof gold/silver/oil coupling caps, silver wire, etc -- but with the shipping risk & hassles for these components, I'm going to need another reason to send 'em in. E.g. I think there's an intermittently sticky relay in my Hera II; if that gets worse, and I'm still gainfully employed, it may be time for a new relays AND Mundorfs.
Enjoy your decision making process; you've got two truly fine choices going here!
Mike