Engine swap 6th Gen: compatibility, PC-V, PAIR, O2?

Hi All - I’ll try to make the story short…

I bought a 02 VFR with 38k miles, and within a few weeks found out the engine was dead (Cylinder #3 all scratched inside, it seems something fell in there), and no CEL. Refused to let her die without a fight… so… Bought a 2006 engine from a crashed bike on Ebay (5k miles), and I’m installing it. (It’s a fine line between bravery and stupidity!)

The bike had both O2 sensors unplugged, and no snorkel. I’m not sure what was the status of the PAIR valves or the flapper valve - I did not take off those parts, so I don’t know how it was. The bike had a PC-V on it (Power Commander V), and a Staintune exhaust. I sent the injectors to be cleaned and found injector #3 had 10% less flow than the others, but they are all fine now.

Now that I’m re-assembling it, I’m wondering:
-- Are there any electronics I need to update to have the 2006 engine running normally in the 2002 frame? Any adjustments?
-- Should I re-install the PC-V? Why?
-- Should I re-connect the O2 sensors? Why?
-- Should I reconnect the PAIR or flapper? Why

The objective is a nice reliable VFR without lean conditions. No track or racing it. I truly appreciate any and all opinions / advice – thank you in advance.