Hey Tot – I am wondering where you found the photo with the .006 relief for the truss rod. Most photos that I have seen are normally between .008 and .010. At .006 my guitars would buzz like a bee hive. My electrics are set up at .010 and my acoustic is presently sitting at .013. My action is 6/64 on all guitars. Anything less than this, once more my guitars buzz.
You have asked very good questions. I understand that new strings or a step up or down in size would effect string tension, which would have an equal effect on the relief. Both of these factors would impact the intonation. From what I have read, even a change in temperature or humidity can throw off intonation.
Guitars:
Electric: Washburn HB-30, Squier Tele Custom Deluxe, Jay Turser Strat.
Acoustic: Seagull S6.
AMPs: VOX AD30VT, Peavey Envoy 110.
Modelers: V-AMP 2, Digitech RP-100A.
Pedals: Boss RC-2 Loop Station, Boss CE-5 Chorus Ensemble, Digitech Bad Monkey, Ibanez DE7 Delay/Echo, DOD VFX40B 7-Band Graphic EQ, Ibanez CS-5 Super Chorus.