Re: SSR ... SHIELD ...strategic homel ... wait
I don't think there's any continuity issues there at all.
The SSR, the Strategic Scientific Reserve, was the predecessor to the agency during WWII (the comparison can be made to the historical OSS being the forerunner to the CIA); then, after the War, the agency was repurposed and expanded as the Strategic Homeland Intervention Enforcement and Logistics Division. It's been that way ever since, operating in the shadows. The name isn't supposed to be new, even in IM1; just awkward and clunky. (As Ward says in AOS, "It means somebody was trying really hard to make the letters in 'SHIELD' stand for something.")
However, there *is* a possible continuity error there that needs to be addressed involving Howard Stark. In IM1, Tony Stark has no idea who SHIELD is; and that's a strange thing, considering that his own father founded the damn agency. Howard kept lots of secrets from Tony; but heading up SHIELD for all those years....? That's a pretty big secret to keep buried from your own family.
THE COTTON AVENGERS
...They move like slick cotton on oil.