Back in the old day, the filecards were EVERYTHING to me. It established what the characters did and stuff. The cartoon portrayals, for the most part, weren't my cup of tea. The Marvel comic was so-so. The DD Comic, 90% didn't float for me. And the movies? NOPE. Therefore, there is no Cobra-LA.
I do, however, reference the cartoon stuff but my world is much more modern/slightly futuristic sc i-fi. The cloning, monster creations, failed experiments, etc. Like you guys know that movies like Aliens, Doom, Predator, and even Star Wars and Star Trek have more influence than the comics and cartoon combined.
As for Lifeline, until I get a good figure of him, he really doesn't exist. Or he retired or whatever. I usually have it so that ALL Joes have basic medical knowledge. They can splint a broken bone, put in IVs, etc. I don't need a special character that says "I AM THE DOCTOR!!!" Ain't no real doctor in Doom, y'know?
As for ranking... Colton and Hawk are on equal footing which leads them to butting heads quite a bit. Duke is the field commander who ALWAYS seems to be injured or out of the picture. lol. Major Barrage, Lt. Graydon (my custom) and Flint are usually the field officers. FALCON would play a HUGE role if Hasbro would make him!!!
When I make up my squads, it is very specific that I would have some sort of leader. So in THE ISLAND, Graydon is top dog. Scarlet was next and then, Luke Ellison's char since he was the 'natural' leader for the Steel Brigade. At the same time, in that story, Graydon was supposed to be there as an observer and Scarlet was supposed to be testing the 3 Steel Brigade members. The Greenshirts in the dio were also under Luke. (forgot the guy's name)
But in Transformations/War For Territory... It was Graydon on top, then Stalker then Beach Head. If those 3 got knocked off, I don't really know who'd be top kick. The ranking is dependent on the story involved.