CDP/Preamp/Amp

In my system I opted to put a good shielded cable on my DAC. I chose the Oyaide Tunami GPX which I purchased from Audio Excelence AZ ($395 including cable cooking and double cryo). You might be able to by one a little cheaper from Take 5 Audio. This cable would be a good option for your CDP IMO, then you can use the Harmonix cables on your preamp and amp. If the Tunami is still above your budget, I have also had good luck with a VH Audio Flavor 4 on the digital source. These can be had for around $300 depending n what type of ends you choose to ahve the PC terminated with.

The order of priority IMO (using separates as you intend to do) would be:

1.) Amp, or power regenerator first (if you use one) or in your case, your Audio Magic power filter, and then your amp.

2.) DAC (or CD player if you use a one-box player)

3.) Preamp, then analog stuff (phono) then tuner

4.) Powered subs or speakers.

Now I'm gonna contradict myself -- because you have a limited budget for new cords, and because the Harmonix will be your best ones for a bit. So I'd make a slight modification: Put the Harmonix on your amp, and on your DAC. But do get a decent (meaning 10 AWG) PC for your Audio Magic. It doesn't really even have to be shielded, but it should have big conductors. Recommend something like the Aural Thrills Silver Big One (used or on auction.)

You didn't say what kind of preamp you'd be getting but I'd rather see you get a good quality, shielded, 14 AWG cord (like a Purist Musaeus) than a poor quality 10 AWG cord whether shielded or not.

Your Onkyo probably has a hardwired cord, so that's not an issue.
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Pre amp is a Bel Canto SEP1 - single ended triode
Amp= Bel Canto SET40-

Better cords on the the amp and cdp? I would have though cdp and pre.