For step 1 simply overwrite the existing files with ones provided by you and leave the same name for the root certificate and key ?
Also regarding the password file what it is its purpose ? should I use another password there ?
the password is used to encrypt/decrypt the key. You can use your own.
And for step 2 you simply renewed only the existing certificates ?
In my setup I want to replaced them also with personal ones generated by my CA server not UCS. Is it possible ?
if you use your own CA server I think you need to understand well how PKI works, so that you can integrate your own CA with UCS (and troubleshot issues). I am not that fluent with PKI so I just stick with UCS CA.