I'm about to buy a bunch of high quality cables from deathvalleycablecompany.com and I'm able to choose custom lengths. I know that its best to keep the cables as short as possible to minimize tone loss.

If you have true bypass pedals in front of the amp, wouldn't all the lengths of the cables add up to something too long? Say you have a 13 ft cable from your guitar to your first pedal, then a few patch cables (say 3 ft overall), then a 13 ft cable from your last pedal to your amp. That's 29 ft of cable all up!

What lengths do you guys use?
29 feet ain't too bad, it more like 50 feet where you really see a difference in sound

also pedals will act as a buffer unless they're all true bypass and all off
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You're correct that a true bypass pedal will mean a longer cable run without a buffer.
You can either add a buffer at the beginning of your chain, or you can just deal with the high end loss.
Honestly, 29 feet of cable is not much at all. A lot of people use a 20 foot cord from the guitar to the pedals. You might notice a little bit of signal loss, but I would not be surprised if you didn't.
Things to keep in mind:
-High-end attenuation is not necessarily a bad thing. If your guitar has a bit too much treble spike for you, a long cable can help tone it down.
-Better cables will do one of two things - make the situation better by losing less signal, or make it worse by allowing you to hear the loss more clearly.
-If you've got a pedal on, you won't hear any signal loss in 13 feet of good cable.