Im not 100% sure about defconf after factory reset on CRS devices but it should be similar to Routerboards i guess. That means the ip address (defconf: 192.168.88.1) you are using to connect to the mikrotik is bound to the bridge. If you remove one or more ports from the bridge you wont be able to use these ports to connect to the routers ip. If you are able to use one of the other ports to connect to the CRS you would be fine. You should first remove both ports from the bridge, add bonding interface with these two interfaces as slave and at the end add the bonding interface to your internal bridge.