Doesn't matter if it's a 5.2 or 5.9 they both had the head cracking issues. Now some will tell you that it isn't a BIG issue but I've seen it enough times now that I would replace the heads of any engine I was installing unless it already had aftermarket heads. And that is always a possibility with the amount of cracked heads.
If you can find a PCI PCM for a manual trans then no you wouldn't have to send it to B&G but the are like hens teeth so unless you have one already I'd just find a good auto tranny one and send it off.
The main issues with the 5.9 being less desirable than the 5.2 is that it runs hotter so cooling it can be more of a problem but it isn't impossible. The 5.2 revs faster but the 5.9 has a better bottom end torque.
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On paper it doesn't look like the 5.9 adds that much but if you'd driven one in a Ram truck the 5.9 has a LOT more umph. Now if you can find a R/T version it's a little better with more power and such but again are getting harder to find.