Hi @LukeSkyWalker , thanks for posting your question here in the Community.
I suspect your switches have some particular VLAN configuration applied to their ports. It looks like you will need to review your switches VLAN design and think your Access Points VLAN accordingly.
As per MR36H datasheet, your MR36H features a "Pass-through port.
MR36H has a unique port which is called Pass-through port, which links directly the second port on the back in the first physical port on the bottom of the Access point. This ports works similar to an extension cord, meaning it will physically link the input of the back port to the output of the bottom first port.
The pass-though port it is a physical extension of the lower back port."
So the ports are like a bridge and would belong to whatever VLAN is configured at the switch port, if the port is configured as an Access Port only.
As you know, AP Port Profile is a feature that allows the MR to extend the SSID to devices connected to the AP LAN Access Ports. Basically, AP port profiles map an SSID to a wired port on an Access Point.
I'm assuming you are connecting your IP-Phones to MR36H LAN ports 2 to 4, hence, your phones would get either a VLAN mismatch or a VLAN double tagging, depending on how the old Cisco switch port is configured.
Regarding the APs connected to Catalyst Switch entering repeater / bridge mode, this is typical behaviour when the AP management interface IP and VLAN don't match the switch port; in some cases, it's just a bad ethernet cabling issue (i.e.: Rx and/or TX pair is damaged but PoE pair is fine).
In summary, I highly recommend you check with your sales contact and have a discussion with a Network Architect. You need to review your current switch ports VLAN configurations and probably redesign your VLANs and WiFi SSID vlan association.
If you found this post helpful, please give it kudos. If my answer solved your problem, click "accept as solution" so that others can benefit from it.