Only the IAP-9x series has a limitation on the number of IAPs per group (16). The 64 IAP per group was an old "suggestion".
You can have all 100 in the same group (must be in the same vlan) then log into the VC, check to see that all 100 are represented in the UI, go to Maintenance, Convert, point to the IP of the controller, then click convert now. The controller should push controller based FW to all the IAPs.
Remember, now that they are controller based you will need licensing on the controller.