Wow, it seems like you have put a lot of thought into this.  I think you guys are trying to make this more complicated that it actually is.  With out any units attached to anything it took me a little while to figure out what was going on, but here is my take on things. 
  
The first equation 
  
CFM flow x cylinders x .257 = HP 
  
I think this one is great, in about to seconds you can guess the HP of a high performance engine.  the constant .257 i assume is determined with the energy released in gasoline at max power rich formula, an average rpm, and an average efficiency of a high performance engine, constant air intake temp, yada yada.  basically a "guess" of what all other variables are gonna be. 
  
The second part 
  
Boost in PSI x 14.7 = additional horsepower.  All this means is that you are assumming that on average you gain 14.7 HP per PSI of additional intake pressure.  Which is why your numbers are different for intercooled and non intercooled setups.  i'd be willing to bet for non intercooled lower boost (3-6psi) you're only going to see gains of 12-13 HP/psi and on the much higher performanace applications (intercooled and what not) your more likely to see 16-17+.  I think that your equation would be more useful for determine how efficient a turbo setup is, rather than guessing HP.  Instead of guessing HP you turn it around and solve for HP/psi 
  
For example: 
  
start with a 300 HP NA engine 
  
and you get 450 HP turbo charge with 10 psi 
  
450-300 = 150 HP/10psi = 15HP/psi 
  
now let say we add an intercooler and get 460HP and our boost drops to 9psi 
  
460-300=160HP/9 psi = 17.8HP/psi 
  
Does anybody see what I'm gettting at or am i just rambling on?