Like you, I'm using Paradigm speakers (Studios instead of Monitors, so it's not exactly the same). I would probably have chosen the settings that you are currently using for the speakers that you have. You may want to play with the mains at 80Hz, though, just to see what difference it makes. Play with the crossover for the mains and possibly the sub trim using some familiar material and see what you like.

Also, did the Yamaha have any sort of "bass boost" mode that you had been using? If so, that may be why you are noticing a difference.

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