What a disappointment to lose your TB bus based on SLEEP failure, then have to go through that extensive restore procedure!
The following information is based on my Z390 Aorus Pro with a flashed GC-Titan Ridge AIC. Flashing was done per @CaseySJ
mini-guides. I'm running fully updated Mojave 10.14.6, BIOS F11, Clover 5107, i9-9900K, RX-580 (headless), jumper cable between the GC-TR AIC and DP on the RX-580. Apple TB Display with the TB3->TB converter plugged into a GC-TR TB3 port, and the other LG display plugged into an HDMI port on the RX-580.
The attached Aorus Pro BIOS - TB.zip
file contains three jpg files (BIOS-TB-x) with screen shots of my BIOS setting for Thunderbolt.
Also a file - AP_04_25_2020 - saved from my BIOS with my current BIOS settings. You COULD SAVE
your current BIOS settings to a file (in the EFI partition of a thumb drive), and load my BIOS setting to see if there are any other settings that might make a difference.
Finally a screenshot of my Clover Configurator Acpi screen with a "Disable GPE.TINI - TB3 Slow Boot" patch that significantly increases boot time with the GC-TR AIC installed. Credited to @Elias64Fr
. (Since you are doing a lot of rebooting!)
Are you confident that the flashing of the GC-TR AIC was successful? Would it make sense to re-flash the card if none of this information I've offered helps?
It seems that typically two seemingly very similar hackintoshes can act very differently.