I think I'd be contacting Banks and asking for their opinion. As much as I'm not a fan of Banks stuff, they are a huge company and have customer service for this kinda stuff.
And then maybe you should be asking Bob to be a little more helpful towards you in communicating. Or.....maybe Bob isnt very knowledgeable or smart enough to call Banks either.
As for everything else..... The pyrometer thermocouple should be tapped into the exhaust manifold, as you said yours is. On the left exhaust bank too which will read from the three back hottest running cylinders.
Boost can be tapped in many various locations. Given you have a Banks system, I'm sure its in a correct location.
transmission temp is a good tool for keeping an eye on your transmission health. Keeping the fluid temps no hotter than around 225* is the key. Normal around town stuff should be much cooler.
Fuel pressures are going to be determined by the type of fuel pump you have, fuel line size, and type of fittings. Optimally you want your fuel pressures to never fall lower than around 14 psi. With a quality aftermarket fuel pump set up correctly, to achieve this would mean the idle pressure is going to be around 18-19 psi.
In regards to EGT's, I'm not sure what you're seeing or what Bob thinks the problem is, but nonetheless the normal EGT's for a stock to mild powered engine will read around 600*-700* cruising along at 70 mph unloaded. Around 800*-900* towing on flat ground. And around 1000*-1200* on the hills.
Now those EGT's are just average numbers and not everyone see's the exact same thing. EGT's vary considerably to and is not a slow reaction gauge.
Maybe you need to explain what the "problem" is that way some here can help you.....