Adamantium bonding, Darkwind, and Bullseye: a theory
So there's been a lot of confusion about adamantium bonding and Bullseye's skeleton and contradictions between marvel bios and the comics so I thought I'd take a crack at it.
Adamantium Bonding: At some point in the distant past, Apocalypse independently discovered adamantium, for some reason decided to try and bond it to human bones, and then abandoned the project. In the 1940's, a young scientist and nobleman named Kenji Oyama became obsessive about Japanese pride and imperialism. He signed up as a kamikaze pilot at the end of the war but survived his run but with a severely scarred face. He found this, along with the surrender of Japan shameful and he started a Japanese imperialist cult on a private island with the desire to get even. He scarred the faces of his children in a similar way to his own and began referring to himself in the western way as Lord Darkwind, always hiding his face in shame.
Sometime in the early 60's someone brought him an adamantium skull. Seeing the possibilities and using the secret, darkest teachings of mikkyo, Darkwind devised a way to bond adamantium to bone in order to create a super soldier but for certain practical reasons, never bonded ribs or fibulae. In the late 60's, spies discovered his work and Weapon Plus agents stole his designs but didn't have the mystical knowledge, thus limiting bonding to individuals with enhanced healing.
In the mid 1990's, one of Darkwind's criminal trafficking operations was raided by a young Bullseye, the entire guard was killed and a young Lady Bullseye was inadvertently rescued. Darkwind began observing Bulls as an ultimate warrior. Upon learning that he had been crippled, Darkwind decided to kidnap him, heal him, bond him, and then insist on his services as his ultimate weapon.
How did Bullseye survive the bonding process?
Bullseye's spine and body were healed with mystical herbs and techniques, allowing him to get up in his prime just a few days after his operation despite having spent several months immobile.
How do you know that certain bones are bonded?
Nearly every major story arc since Daredevil #96 addressed the metal skeleton in one way or another. The only bones he has been shown breaking are his back leg bones and ribs after being hit by a bus at the end of the Murdock Papers.
Does Bullseye have a healing factor?
No. His skeleton offers him added flexibility and protection but he is still susceptible to brain injury, blood loss, certain broken bones, organ injury, etc.
Why does Bullseye heal so fast and why isn't he crippled at this point?
You've seen him impaled, skewered, shot through the hands, multiple body shots, etc. First of all, his skeleton is adamantium bonded, second and his suit is made of woven kevlar dense enough to protect against small arms fire, and to minimize damage from assault rifle rounds to the level of flesh wounds. Second, up until he was extorted by Deadpool, Bullseye was a well known and extremely frugal assassin who had built up a hidden personal fortune rivaling Norman Osbourne (to the tune of several billion). He had better than the best health care money can buy and after he joined the Thunderbolts up until DD killed him, he had Norman's implants and nanites making lightning fast repairs.