The compressor motor stopped running,(I was told it was bad) so I replaced it. When I started the unit back up it ran for a few minutes, but when the compressor tried to kick in it shuts off. I tried it several times but whenever the compressor tries to kick in it keeps shutting off. They gave me a compacitor when I bought the motor but it was different than the one on the unit. The one on the unit is a cylinder with three poles, the new one is short and oval and only two poles. Could this be the problem or is it in the compressor.

You have it (the capacitor) wired wrong. Look on the side of the motor it will have a wiring diagram