Hello Ashley,
You will have to engage Cisco professional services. They have internal tools that help merge multiple configurations so you can migrate to the lower number of instances on the FTD
Your tool is the latest already. I would recommend to upgrade the FMC to 6.2.3.3 patch so that the tool can push bulk objects. That would be much faster.
FMC 6.2.3 does not support bulk push for objects. While the migration should work, it may be quite slow. I would recommend to upgrade the FMC to atleast 6.2.3.3 patch for a faster migration experience.
May i know your FMC and tool version?
From FMC 6.2.3.3 onward objects are pushed in bulk (1000 in one call) which should be much faster than it was before.
You can use the console window of the tool to verify which ones are currently being pushed...
