Well i have been teaching myself c'mon girl by the red hot chili peppers and i just cant get the notes flea plays for the main riff quite right. i mean i can play it decently fast but its all inacurate. Do you guys know anything that i can do to perfect this song
i have been practicing every scale i know up and down the neck on a metronome increasing speed as i go along will this suffice with practice or what?
Slow down. Get it perfect at lower speeds. Gradually build up.
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Yes, slow it down. If you continuously try to learn it at a faster tempo all you'll get is a sloppy riff. If you slow it down to where you have it perfect and then SLOWLY bring it up to speed, you'll be much better.
Do you have a reasonably accurate tab for the bass line, or are you just learning by ear?

With the tab, your best bet would be (as has already been said) to practise real slow, and then when you have the part and phrasing stuck in your head, speed up.
And then just keep rocking it.