The Calabash port can now be changed on per-app basis by adding the following triple to the app's Info.plist:
CalabashServerPort NSNumber < port number >
You are still going to be limited Apple's restrictions on the instruments process: there can only be one active instruments process. Further, the instruments command line tool will not work if the Instruments.app is open.
Other posts have recommended using VMs, but I have no experience with this.