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@polybikeuser
Let me start by saying I'm not a frame builder, done quite a bit of research and thinking about frame geometry in preparation for ordering a custom low-pro, but I've never built anything.
As far as I can see bottom bracket height is usually specced in terms of bottom braket drop, i.e. how far it drops below a horizontal line drawn between the centre of the axles of your wheels. A lot of adapted for street track type bikes have a drop of 60mm, e.g. the FBM Sword and Geekhouse Rock City, the Soma rush is slightly higher with a drop of 58mm, so 60mm seems like a good starting point.
This is just a thought, but where did you get your figure of 59.5cm for the seat tube? Seems a bit risky to be deciding on seat tube height independently of bottom bracket drop. If the bike your basing this on has a different bottom bracket drop to what you spec for this bike it will change the height of the top of the seat tube, so changing standover height and amount of seatpost sticking out for a given height. So to guarantee you get what you want you need to reference seat tube lenght to bottom bracket drop.
From what I've seen chainstay length seems to vary between 390mm-400mm, so if you want the rear wheel right up close to the seat tube, go for 390mm, you want maximum clearance for wider tires, go for 400mm, or go for the average 395mm. Don't think absolute chainstay length is critical, after all you can move a wheel back and forth a good 2cm in a horizontal drop-out.
Fork rake is the thing I know least about, not enough to offer a competent opinion, ask your frame builder? Good luck :)