Repaired the diode, finished the two connections and it hasn't blown yet. 
(But it won't start) 
  
I have loaded MSnS-Extra (can't find MSnS) and I set it up.  It connects and interfaces with the computer. 
  
Everything is now set up except for the fuel pump. I put it on the wrong cable on the original harness, so the fuel pump relay is not getting power. (Easy fix) 
  
I get everything except the coolant temp sensor (It is dead I found out, if I short it MS displays temp, so it is a bad sensor) in the MegaTune display. 
  
I get vacuum, rpms, pulse width, and spark when cranking. I think I flooded the engine (I get a fuel smell, I think the fuel injectors are firing, I will check tomorrow) 
  
Why won't it start?  Because I got rid of all the TB air bypass and wasn't opening the TB (do'h) 
  
Hopefully it will start tomorrow, now that I think I know whats wrong with it  
  
Thanks, 
Mario