Adam, it isn't entirely clear how you're defining "disconnect" and you're getting varying responses. Are you experiencing a substantial variation in output level or is it instead a variation in tonality? If it's the latter, as Randy pointed out, you have to keep in mind that the center speaker is of significantly different design and will sound different; this is one of the reasons why the ideal would be to have a center speaker identical in orientation and as identical as possible to the mains in frequency response.
The several points that you list don't appear to be major problems: the separation is just slightly wider than usually suggested, but should be okay if you have enough toe-in so that the tweeters point at your ears; the level calibration that Audyssey did should be reliable if the instructions were followed and it's unlikely that adding human error by way of a manual calibration with an SPL meter would result in higher accuracy.
