All airlines shown on the series are actual airlines. The lone exception is Yamato Air Lines, which was created for the show (as a good deal of the plot revolves around it.)
Some stories/characters/situations/etc. that were not used in the manga were later used in the 2004 adaptation of the story (for instance, hearing the word "gold" over a radio transmission leading to a wild goose chase of sorts.)
Nearly every plot point/event from the OVA is taken straight from the manga. Despite this, almost all of the events happen in a different order. Some plot points have been combined, as well (for instance, shooting a bomb off from a Yamato Air Lines plane and Ryoko and Yasuda's being on a plane heading for Asran were two distinctly different events in the manga, here they are combined).
A major subplot of the manga that did not appear in either anime adaptation was Ryoko adopting a French orphan that she finds in an airport, who is in the midst of a family conflict.
Characters that appear in all 3 versions of Area 88 (manga, 1985 OVA, and 2004 series) include (but are not limited to) Shin Kazama, Satoru Kanzaki, Mick Simon, Greg Gates, Saki Vashtar, Roundell, Boris, and Miss Yasuda.