As you know every new component in a chain will result in a different system response. I think adjusting distance to rear wall and toeing the speakers in/out should suffice.
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I think you can affect the tonal balance with speaker placement and that if you are hearing that big of a difference (i.e., the upgrades caused that much of a change in sound), then it may be worth playing with speaker placement. (of course, just changing the calendar over to a new day is excuse enough for some of us to tweak).