The Options Missing message is just warning you that the AutoCal is not set up correctly for reading, flashing or logging. You can re-setup your AutoCal for the controllers that you want to log, read and flash using the [F5: BBX] option in the EFILive V8 Scan and Tune software.
When you have selected all the controllers you want to read/flash and all the controllers and PIDs that you want to log, click the [Program] buton to re-program all the setup info (including the Options.txt file) to your AutoCal device.
Second problem sounds like the AutoCal has been changed from the simple menu structure to the advanced menu structure. You can change it back again using the [F6: Devices] option in the EFILive V8 Scan and Tune software. Open that option, click [Read] to read the current settings from AutoCal. Then choose either the simple or advanced menu option on the [F5: Options] tab page. Once you've made your selection, click the [Program] button to save the changes back to AutoCal. Wait 5 seconds to allow AuotCAl to save the updates, then power cycle AutoCal to get it to recognize the new menu option.
Regards
Paul