I hope you figure out the metal grinding noise.
Find out if you have the Lexus kvafm or not. It's important.
Disconnecting the SAFC2 wont change the settings ("tune") unless you physically reset them, not sure about the SAFC1 but they aren't much different. You really don't need it but they are cool. If you think it's a problem just rewire the afm back to stock, the safc doesn't affect anything else.
As for the codes, I would check the grounds under the intake first.
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