What we have here is a real cluster f*ck!
But you are also a little confusing......
"The 01 na ecm will fire the engine but no pulse on the injectors."
then you say......
"The 01 gets the wake up wake signal but does not send the crank signal on yellow black wire that cranks the engine."
So which is it? Does it crank and not start, or doesn't crank at all?
Let's go over a few things......you removed the SC'd engine and PCM from the '99, and installed a VIN K motor and PCM from an '01 engine, into the '99, correct?
Do both vehicles have the same SECURITY system?.....you say the '99 has a black pellet on the key......is there a black pellet on the Key for the '01?
If yes, then check the resistance of the '99 key, with the resistance of the '01 key......only a 1 in 15 chance they are the same.....so if they are not, go to a locksmith or GM dealership, have them read the R code on the '01 key.....then buy another key with that same R code, and cut it to match the '99 key and then see if the car starts.....
If the '01 key does not have a black resistor on it, than we have two different SECURITY systems here...
But this bugs me:
"The 99 ecm for the sc will crank the engine with spark and injector pulse but will not fire the engine." If you have spark and compression, and fuel pressure, that engine should start........were there any codes?