[LS short box]

I always run a adjustable prop valve with my disc/disc swaps because I don't typically build anything stock.
I'm working from memory so that's more than a bit scary but I seem to remember that an adjustable prop valve doesn't limit the pressure to the rear just slows the application down some how or another. I use Wilwood prop valves. Just the simple one that has one line in and out for the rear line. Not the best pic but you can see the prop valve below the master.
Again I'm far from a brake expert but with your combo I would delete the stock prop/combo valve.
So my go to guy on brake systems is Tobin at KORE3.com. Call him and tell him what you got and he will tell you what you need. You might not like what he will have to say but he a brake expert.