Ok so I got the above the second run through some how. But I also found an even BETTER place to get fast points and DNA.
Play through SCENE 23 until you are destroying the waffle irons that produce the clones. After the first Quantonium machine is destroyed, head through the door and there are some crates on the right side. Destroy them and take the pinball jump up to the platform with the missile command machine. Now place the target just to the left of but NOT ON the waffle iron and start shooting. The clones will come out and you will blow them to smithereens with the missles. Rinse, repeat.
I prefered this method over the spaceship method above because a) The spaceship moves around on you and you have to track it a bit and b) sometimes a robot will make it over to you and start killing you. You are now free to hit (A) and ignore the game altogether.