Total: $448.93 after $9.00 shipping and $10 promo code (before $15.00 mail-in-rebates).
You won't be able to fit a fast GPU into your budget. You can't fit most of your requirements into your budget. You could step down from the i5 to this i3-2120 and come in at $388.93 (after shipping, before rebates) without a GPU, though. You can always add a GPU later if needed, but since you're using Linux, I'm assuming you won't be gaming, and therefore the onboard video should be fine.
If you give me some more information to go off, for example what you're using your computer for (instead of just needing it to be "fast"), I can probably give you some better advice.