How did Arcane survive thousands of years here on earth with Gills? From 1987 until 4000 to 5000 AD on the present timeline we are on? And past 7000AD on the first timeline?

Much easier than you might think. HE decided to leave his gills and his amphibian underwater breathing genetically designed body in this form because it would be hard to change this and not worth the effort in the long run. But, he did remove the webs between his fingers and toes and shorten his tongue and move his skin away from being purple and change his eyes from being Metallic Golden that reflects the sun with Contact lenses. So, he actually still has the golden irises because who wants to have an eye operation just to come to earth. Shortening his tongue was enough and removing the webs from his fingers and toes was enough and changing his skin from purple to white was enough to pass for an earth born human even in the times of Francis Bacon in the 1500s and 1600s. 

Besides, his human genetics originated on earth now in the 2000s to 2500s before they started colonizing other worlds in the first place. Remember, he is from around 1 million AD where he was born and traveled back to live here on earth after being Trained by Eridian (Meridian) 1 million years into the future.