Attack Potency/Striking Strength/Lifting Strength
Dan scales above 100 times Danny's 8-A (533.70 tons) feat which would make him unqualifiably above 7-C (53.37 kilotons).
Johnny X scales above is base which scales to 7-C (50.3 kilotons).
While neither have a significant lead, Dan has Reactive Power Level which would boost his power to the point were he'd be able to effect people who could completely tank his blows without flinching. Tie in his Statistics Amplification via adding his ectoplasmic energy which also would allow him to tare through people on his level.
Lastly, Rage Power gives him a boost as well so I don't see how Johnny is going last long. Also Dan has the higher lifting strength so he's going to be manhandling Johnny. Johnny may be able to buff himself with the Super Strength Milkshake but Dan has more buffs so he'll stay ahead.
Speed/Agility
Speed is Equalized, and both have acrobatic skills so neither hold any advantage here.
Combat Skill/Experience/Intelligence
Johnny has better hand to hand combat skill (skilled in kung fu and a black belt in karate). However Dan has the experience of both Danny and Vlad, plus has fought Valerie Gray who is also a black belt in karate. In overall intelligence Dan is superior, but Johnny can increase his intelligence with the Super Smarty Pants but I don't see that actually helping here.
Stamina/Endurance
Johnny can go for hours to days before getting tired but Dan has infinite stamina due to his Ghost Physiology so he isn't going to slow down throughout the entire fight unlike Johnny who'll eventually get fatigued.
Range/Area of Effect
Neither seem to have a massive range advantage over the other besides Dan's Interdimensional range.
Abilities/Resistances
Most of Johnny's abilities are useless against someone like Dan since his Body Control will allow him to avoid anything small, and his Regeneration exceeds that of Johnny's to the point where Johnny can't bypass it. Both have Teleportation and Telekinesis, Dan has BFR which Johnny has no way back from.
As for Susan and Mary's gadgets, nothing can really help him here. Time Travel, Time Manipulation, and Time Stop all get countered by Clockwork's time medallion. And even if he didn't have Clockwork's Medallion, time stuff wouldn't really allow Johnny to win, at most it would give him an Inconclusive since he still can't put Dan down or incap him.
Johnny's Memory Manipulation, Mind Manipulation, and Possession all get hard countered by Dan's resistances. Meanwhile, Johnny has no resistance to Dan's Possession. His Transmutation can be countered by Ghost Physiology since Dan's ghost body is just a construct that can be reshaped even after being altered.
Johnny's Gravity Manipulation, Smoke Manipulation, and Sleep Manipulation all get countered by Dan's Ghost Physiology and resistances. Both have Duplication and Invisibility so it's not an advantage for either.
Conclusion
Dan stomps in my honest opinion.
He'll easily exceed Johnny's strength with his Reactive Power Level, Rage Power, and Statistics Amplification. He's overall more experienced than him and has battled enemies with Johnny's level of skill before, and he doesn't fool around against others unless it's Danny.
Majority of Johnny's abilities get countered by Dan's Ghost Physiology, resistances, and Dan has several of Johnny's abilities already and vise verse. Meanwhile, Johnny lacks the resistances needed to stop Dan's abilities like Durability Negation (phasing or ectoplasmic energy on a molecular level), Possession (on a molecular biological level, mental level, and spiritual level).
The best I see Johnny doing is stalling and irritating Dan at most with Toon Force but eventually, Johnny will get tired and Dan will defeat him. The only possible way for Johnny to win is if he uses that Casualty Manipulation offensively in character which I doubt.
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