Thank you, yes, I have followed the instructions and videos at the link you provided. So where I got stuck was second video showing AC where you press remote button and create a node. I pressed remote buttons and no nodes are created, no matter what remote I used (Harmony or regular IR remote).
After experimenting and reading some posts on the Flirc forum, I added a new "Device" into the Harmony software and then I was able to easily create nodes in the eISYIR Node Server. Once I had those nodes, I was able to modify my Harmony Activities and my IR programs migrated from ISY994i IR to work as they did before migration.
jpoje's post in Looking for IR and/or Harmony Advice was marked as the answer