We know of at least 2 Ridleys, if not 3 or 4 really:
In Zero Mission, we have Ridley 1, the original biological Ridley. You also have robot Ridley.
The following event, Prime 1, had Cyber-Ridley (With ZM's retelling, I like to think the cloning division and the robot crafters had a meeting and decided to just mix what they had left of Ridley 1 and robot ridley and make a whatever the hell it was.
Skipe prime 2
In Prime 3, Ridley was entirely biological, but was also Phazon infused.Phason alters the biology, so even if mecha ridley, being re-healed in an entirely biological creature, he would not be clonable from a phazon altered Ridley. I think at that point, the pirates decided to screw it and just start cloning Ridley.
Skip metroid 2
He came back in Super Metroid, fully biological and much closer to his Zero Mission level of ability. He was defeated mere moments before the planet was blown up. It was implied that no space pirates could have escaped the destruction of Zebes. In fact, Metroid 3 was the end of the space pirates. Mother Brain was blown up, their super secret secret home base along with the ground under it was vaporised.
Ridley's body was seen frozen in Fusion, but it could not be dead, since X mimics living organisms.
Also, when was the first time the federation in contact with Ridley?
Prime 1, on the frigatte that was attacked by the pirates... a federation frigatte, cloning gigantic murderous creatures (parasite queen?). On the frigatte, it was a Ridley that also happened to be fully healed. The first contact between Ridley and the federation. The second time was in Prime 3, during the battle, but that Ridley did not die until his later incarnation.
But again, how was Ridley present on a federation base once more?
Also, at that point, the Federation must have gotten data on Metroids, I suspect their involvment predates the larva incident simply because federation ships have been found on 3 planets where metroids had been brought by Samus, one of which wasn't blown up to bits. In fact, thanks to Prime, we can safely assume the pirates have other Metroid study facilities.
Also, would the space station in Fusion be the only metroid research center?
Finally, who had the idea of using Metroids as power source?