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Try first to start in SMC bypass, just in case.
Be sure to use original Magsafe 2 charger; better 60/85W for test.
Also post PM_BATLOW_L, PCH_DSWVRMEN and PM_DSW_PWRGD levels.
"6 = 0V (PP3V3S3_EN)"
Doesn't pulse high?
It should, when PM_SLP_S4_L pulses; output pins must pulse too, check for short.
Check the same on all these chips.
"Also test the MLB alone, disconnecting LIO flex."