1. Vader might not be insanely fast, but in his "prime" he has shown the ability to take out accomplished Jedi Knights with relative ease. He is able to close a distance of 20 meters in "the blink of an eye" in Rise of Darth Vader, and this is only 3 months after Mustafar while he's still struggling to get used to his cybernetic suit. He wont blitz Logan, but his sheer speed is massively underrated. His battle precog will give him the nessecary skills to fight Logan up close, given that he has fought multiple Jedi at once and came away unscathed.
2. After becoming accustomed to the suit, Vader is skilled enough to fight 6 dueling droids set on the highest level of their dueling programming at once, only giving him a moderate challenge.
3. In The Rise of Darth Vader, he takes out 6 Jedi Knights in about 20 seconds. Later in the book, he used his TK to dismantle an entire bridge while fighting Roan Shryne on Kashyyk, sending a "storm of pillars, planks and railing" hurling at his opponent so fast a Jedi swordmaster (Shryne is stated to be a master of the sword in the same book) couldnt hold off the onslaught.
His TK is powerful enough to hurl objects far heavier than Logan at blinding speed. Logan isn't fast enough to catch Vader completely offguard, and Vader is known to resort to his TK when he becomes uncomfortable in close combat. In the OT, he Force Chokes an Admiral in a different sector of space just from being able to see him. Thats a massively impressive feat.
His suit is armored as well, in the OT, the suit withstood a lightsaber strike from Luke's saber with minimal damage. The electrical systems are lightly armored as well, but electricity can short them out.
Im going to assume Vader's lightsaber wont cut through Logan's adamantium skeleton immediately. That gives Logan an edge in extreme close combat. Vader has the reach advantage, his lightsaber is far longer than Logan's claws.
Regeneration would also give Logan another edge, but Vader has fought beings with regenerative capabilities before, but Logan's regen is something he hasnt faced. I see Vader having an edge in brute strength, he is stated to be able to crush durasteel with his cybernetic hands
That being said, Logan's regen isnt unbeatable. In one arc of X-Men IIRC (Logan goes crazy and starts killing off the X-Men) Kitty Pride reduced him to a vegetable by phasing through his brain. Vader could basically do the same thing by crushing his brain inside of his skull. Assuming he decides against that, he could pin Logan using TK and take his time with his lightsaber once he figures out that Logan cant be killed conventionally.
Unless Logan can figure out a way to blitz Vader (unlikely due to Vader's precog, which is superior to most Jedi's) I just dont see him possessing the ability to take Vader out.
Here's how I see the fight playing out.
Location: Star Destroyer Executor
Logan ambushes Vader, sacrficing a deep flesh wound to carve a deep gash into Vader's forearm. Vader is just quick enough to avoid a fatal slash to his electronic systems, and after a brief exchange with Logan at close quarters, pushes him out of melee distance with the Force.
Dampening the sparking around his gauntlet, Vader realizes his opponent is incredibly dangerous. He also notices the gashes on Logan's body healing at an incredible rate. Logan tries to catch Vader off guard by charging straight at him, only to be smacked aside by a steel girder Vader ripped from the surrounding environment. Logan shrugs it off, and gets in close enough to engage the Sith Lord in melee combat for a second time. Vader's precog and brute strength give him enough skill to hold off Logan's assault. Logan goes for his famous lung impale move, only to be caught by the wrists by Vader. Logan loses the grapple, and is flung away by the stronger Vader. Logan goes into beserk mode, scoring another hit, this time on Vader's shoulder armor, actually cleaving through the armor to inflict a wound in Vader's shoulder.
Enraged by being hit, Vader decides that close combat isnt the best tactical option. Using the Force, Vader crushes Logan's windpipe, choking him to "death". Logan eventually suffocates and collapses, seemingly dead. Vader takes a moment to observe the lifeless body of his worthy adversary, and then turns away, leaving the clean up to his Stormtroopers. Logan heals from his injury, and begins carving through the cadre of stormtroopers to lunge at Vader from behind. The Force warns Vader of the danger, and without turning around, Vader uses his TK to catch Logan mere inches away from scoring a fatal blow. Vader then hurls Logan against a wall with enough force to crumple the durasteel around Logan's indesctructable skeleton.
Pinning Logan to the wall using the Force, Vader ignites his lightsaber, and promptly stabs Logan through his eye socket, the lightsaber meeting resistance as it melts through the orbital bone, finally penetrating his skull. The lightsaber severs Logan's neurons, and cooks his brain from the inside out, leaving Logan a vegetable until he regenerates. Seeing his foe return from a fatal injury once before, Vader takes no chances. Using the Force, Vader hurls Logan through the transparisteel window of the Star Destroyer, leaving Logan to succumb to the vaccuum of space, over and over again.
Vader wins, but not in a curbstomp. His TK and variety of long range options puts Wolvie at a disadvantage once Vader figures out his lightsaber wont cleave him in two.