I just renewed our SSL cert last week using the same version of KYRTool without issues. I also used the concatenating process described in 6a Option 1.
Take a look at this page:
http://xpagesandmore.blogspot.com/2015/03/notes-901-fp3-if3-tls-12.html
Search the page for "OID" and you'll see an SPR that was addressed by Notes 9.0.1 Fix Pack 3 Interim Fix 3 that states:
"...kyrtool import all sometimes reports "SECIssUpdateKeyringPrivateKey returned error 0x0720", "AVA separator not found" or "Syntax error in OID" when a '/' is in a certificate name part".
So, if that applies to your situation, maybe update to FP3 IF3 or higher (FP4 is available as Chad Scott notes in his post) and see if it fixes the issue.