Hi 1markr
Yes, I also have a fully modded Berning with all you mention and have tried numerous combinations of input/drivers. The Berning is improved greatly with these mods and the cryoed hybrid wire is probably the most significant in my estimation. It gave the amp a more relaxed presentation and improved the highs significantly. That is to say more effortless across the board.
In truth I agree with much of Rushton's impressions as they mirror my own except for the high frequency presentation of the Joule, it really must be heard with the Merlins to appreciate all the accolades this combo has received. There is a true sense of air above and around instruments and vocalists that capture the reality of a live performance. When I first heard it I couldn't believe it improved so much over the Berning although this was before I did the wire upgrade which markedly improved the situation. What is quite different is the harmonic richness, not an exaggerated fullness as I have heard with many tube amps but a rare combination of harmonic reality plus transparency of the highest order at least the equal of any amp I have heard. The Berning and Atmas-phere excel in the transparency but are harmonically a bit leaner. I have communicated with several Merlin owner's that have heard both and there is no concensus which is better as they each offer a different palatte of musical reality. I would offer this hopefully without it coming across as contradictory, the Berning is more neutral to the recording while the Joule can sound closer to real. As Jim notes the Joule offers greater dimension of the space. I recently heard that gap close quite a bit after auditioning a few pair of Stereovox Sei 600 cables which to date are the only silver cables that I heard truly work with the Merlins. The cables opened up the soundstage and dilineated the instrument lines to a degree of a major component change. The bass was the best I have ever heard the Merlins, taunt defined in space and deep, no bass, no way man! An audio buddy who has watched my Merlin system evolve over the past 4+ years was completely taken back by the addition of these cables and remarked that maybe it was closer to the Joule/Merlin combo in certain areas of spacial resolution and venue reality.
The bottom line is that the Joule/Merlin combo is world class, truly among the best I have heard. The Berning/Merlin/Stereovox system won't make you second guess a thing it is so wonderful. Each offer two different presentations with a differing set of appeals, as Jim notes, it would be hard to part with an amp as special as the Berning especially if you explore deeply and discover what it is truly capable of with the Merlins.