Installing v5033 does not remove the earlier folder structure. All the drivers are now 64 bit and reside in /EFI/CLOVER/drivers/UEFI/. Since the old folder is not deleted, you can copy the AptioMemoryFix-64.efi (and rename it to aptiomemoryfix.efi if you wish) to the UEFI folder.
Perhaps the structure has changed if you do a fresh install with no prior version of Clover in the EFI partition, but I just confirmed installing v5033 does not remove the earlier folder structure. However, you're correct; all the drivers are now 64 bit and reside in /EFI/CLOVER/drivers/UEFI/.
The problem with not booting after installing v5033 no doubt is because you didn't customize the install to include AptioMemoryFix-64.efi in /EFI/CLOVER/drivers64UEFI/. The only thing essential in the kexts/Other/ is FakeSMC.kext.
Glad you got it resolved. Cheers.
I've been running my User folder from a separate drive for ages including Mojave and the Catalina Beta builds. Absolutely no problem other than an annoying message in Catalina that it wants me to convert the drive with my User folder to apfs in order to use i-Cloud. So, since Catalina moves user...
If the drive shows up in the bios, you should be able to select it from the Clover startup menu of operating systems when you boot from the installation usb. You didn't state which MacOS was on the drive you can no longer see. If it's on an apfs volume, and the usb installer was made prior to...
If the MacOS drive is connected and is listed in your bios, it should show up in the Clover startup menu (even if the efi on that drive was trashed by the virus). Suggest you check the bios at boot to see if the drive shows up.
Best to not 'store' these kexts in C/Kexts/other folder because if the kext in that folder is not the same as the one in /L/E it may cause problems. If you want to store copies, put them in a a different folder, such as ~/documents
The Clover log doesn't help resolving why the bios flash screen hangs for a minute or so, since the log only starts once Clover loads. As much as I will regret suggesting this, but can you try booting from a different drive and remove the M2 drive?