Pls note that there is no dedicated Lufthansa check-in counters. All are handled and manned by SK. You should try to check-in online or use the check-in kiosks at CPH airport. There are only few manned check-in counters for Y pax (C and *A Gold cards is different) and the lines can be quite long; altough for these early morning departures the lines are most likely relatively short. There are dedicated counters for baggage drop (when using the check-in kiosks)

If you have luggage to check-in I agree 90 min before dep. should work well. If you have hand luggage only (well, unlikely if you have been on a cruise) and have checked-in online and printed your BP, I would arrive CPH around 45 min before the flight.