By far the best modded Marshall I've tried is my Marshall SLP that was modded by Dave Friedman to the specs of the Cameron Atomica. Apparently it was a one off amp and was made sort of like a prototype to the actual Atomicas. I tried an Atomica once at Tone Merchants and I like mine even better. It's more raw and aggressive from how I remember the actual Atomica sounding. Since getting my Atomica I've sold/traded the following amps (and they were all terrific amps
Bogner Helios 100, Gower Rockmonster, 1968 Marshall Major 200, Metropoulos Metroplex, and a Mezzabarba Mzero Overdrive. These were all killer amps (especially the Mezzabarba and Gower), but I AB'ed all of them several times, and they all for my taste had nothing to offer me compared to the Atomica. The Atomica is also quite versatile with it's 3 voicing switch and diode clipping knob on the back. It had the biggest sound, moved the most air, and had the most complete and raw growl compared to all these amps, although the Mezzabarba was similarly big sounding and the Gower had similarly complete growl on powerchords. And it also had the tightest and most articulate palm mutes of these amps, and was better for leads and single note riffs (the notes had more weight and stood out more). It's tied with my mark IIC+ HRG and mark III++ coliseum as my favorite amp!
I've also owned the following and they were all good but none of them were nearly as good as my Atomica: Friedman Phil X, Henning Cherry Bomb, Langner DCP-1, Mesa/Boogie Stiletto Trident Stage II
I bet the other Cameron modded Marshalls may be every bit as good or even better than what I have, but never got to try a Cameron modded Marshall yet. I have a CCV, but that's not at all a Marshally sound IMO. I also really wanna try a Gower Killer Kali ++ mod
Also, my JCM800 with the V5 mod by kruse is awesome and one of the best modded Marshalls from my experience! By far the best JCM800 I've tried and I'm not generally a fan of the 800's (I prefer plexis). It originally had that custom one off mod done by Friedman for Reza and it was good, but sounds 1000x better now!