Hi Anthony,
Good to see some progress. Initializing Disk 2 will make it visible in windows explorer.
Regarding the install issue, can you download either CCleaner or WiseRegistryCleaner and run a scan a couple of times to remove any bogus registry entries. Run the safe clean option, (not the advanced option). REBOOT afterwards.
Have you ran HP Support Assistant yet? Please try again now the new firmware is installed and detecting the SATA drives.
In the meantime I will do a bit of digging regarding the ME firmware issue.
All the best.