why didn't the founder just put him self in the machine ?

Because Roger could stop time and the Founder couldn't. Basically the only way that the homo-superiors could kill homo-sapiens is if Roger stopped time and thus placing ordinary people in a sort of limbo; neither alive nor dead. The key being not technically alive so homo-superiors can now destroy people with telekinesis.

Why didn't the Founder just inject all of his agents with the kill serum (that we find out he had for quite some time in the last episode) Then they could just go around and take out anyone they wanted. With the superpowers they have, who could stop them?

X ~We are the people our parents warned us about