against Thor, Superman's weakness doesn't really mater much as Thor cant generate red sunlight nor produce kryptonite. Magic doesn't even equate much as Thor's magical nature doesn't add much as he doesnt really use magic offensively like most magic users like strange an zatana. so out come would be the same with IMO Thor still getting the majority
Against Surfer, Surfer can still drain Superman. or he could amp his strength to "Atomic Level" whatever that means 😛 Plus his other exotic powers would still prove adequate to take the Majority
No CIS? Supes loses to either after a good fight. Surfer and Thor are often underestimated uberduber-powerhouses because there's so much CIS in their comics.
With CIS? Could go either way. Superman rises to impossible challenges perhaps better than any other character, so much so that a lot of people really, really hate/love him.
As someone said above this wouldn't change the outcome with Thor as the Asgardian's route to victory doesn't involve weakness exploitation in the 1st place. Supes would edge him the same way.
Against Surfer without the weaknesses I think he beats the Surfer, stronger, more reactive in cqc (certainly a better guy in cqc), great energy durability.
Superman beats Thor 7/10 - Thor has the fire power advantage...But for the rest Superman is above in Speed , Strength , Durability etc maybe not a lot but enough to get decent wins.
Surfer Still wins 6/10 - Close battle they are pretty much equal in everything...Surfer is just more versatile and equally good in other aspect of fight that matters.