Issue number 1, solved with help from KASPERSKY Technical Support
1)Please double check if there still any entry on the below registry keys. If there still there, please remove them.
(please perform a backup if you remove any register)
HKEY_LOCAL_MACHINE\SOFTWARE\360
HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\360
2)If the entry has been removed from the registry, please try to install KES installer with incompatible software detection disabled.
Issue number 2 and 3solved with separate installation, create separate installation package for KES (without network agent) and separate package for KNA. Then install the .exe KES first, then KNA