There is no reason to assume that Deadpool lost any of his abilities after receiving surgery. The entire point of that experiment was to augment him.
I haven't seen anything in the movies that suggests Thor wouldn't be vulnerable to, Adamantium. Aside from a direct kill shot I imagine that, Thor would be able to endure quite a few attacks from, DPs swords, however, it's very likely DP could land an early kill shot, using his swords an teleportation. I think it's more likely to see DP land an attack with his swords sooner than we would see Thor land an attack with a fully charged, Mojinor. I still take, Thor as the winner in this fight but I think Deadpool actually has a very good chance early on