Just a thought, but why not run the 5.9 long block with the 5.2 intake/electronics? I don't think it will make it run poorly, and I've heard of many people running stock/very mild 5.9s on 5.2 computers. I have a mild 5.9 running on a 5.2 computer, but it has been tunes via SCT Flash which you unfortunately don't have that option unless you swap to OBD2.
Mine is mild but I would not call it very mild. EQ heads, Mopars R/T+10 cam kit, 1.7 Harland sharps, M-1, 52mm fastman, 24lb injectors, Gibson shorties. It is at the limit for what the PCM can handle though. There is no difference between the kegger intake on the 5.2 and the 5.9. I have never run into anything that the PCM cannot handle besides camshaft. I have an old 210x cam that I put in when I put the motor together but the computer could not manage it. Hence the mopar cam kit on the recommendation of the tech line at Mopar Perf. back in the day. Like I said for being OBD1 I think I have squeezed about all the juice out of her. I plan on a Holley sniper system with a carb version of the M-1 for the next bullet.