After my LMM swap what to do
 

So I'm planning on a future LMM Duramax swap into my 2010 Suburban 2500 after my previous question of swapping an 8.1L into it fell short with too many headaches. After it's done I'll have the old L96 6.0l motor and 6L90E transmission to deal with.
I have my 1999 GMT800 Silverado 2500 4x4 with an LQ4 and 4L80E that could use a fresh motor and transmission........
So, how best to pull off the new for old swap? Do I use the newer E38 ECM in the older truck? Or should I do a reluctor swap and delete the VVT since I will be tearing into the engine anyway to cam it and freshen it up before it goes into the truck? The new one is fly-by-wire so can I use that or do I need to ditch it for the older cable setup?
What is the best way to gain the power and efficiency of the newer setup without too much headache with wires and sensors having to be changed?

That is about the holy grail of engine swaps at this point, the 6l90 needs the 58x crank reluctor to work properly, but the instrument cluster needs a 24x signal, then theres the issue of the speedometer and ac and a few other functions all of which run off of the factory pcm.... Speartech did it in an 02 and had to build a piggyback harness for the factory pcm to get the dash/ac etc to work.... Would like to figure it out myself i think a 6l90 with the manual t case put of a nnbs with vvt would be awesome in my 99.....