Did you ever consider telling the owner that the mfr's site shows the msrp to be $2800? The owner could indeed be mistaken, or there may be a reason why the msrp is $3500 (different model, upgrades, blah-blah). Your gripe may be reasonable, but your answer lies within the walls of the LBS, not here.
As for the partner quoting $2400...maybe it was tagged @ $24XX, he interpreted it as $2400, but the owner rounded it to $2500. Again, you should ask them; however, I wouldn't bother inquiring further unless I was in the market for that particular bike in that price range.
You haven't handed over any money yet, so there's no reason to feel swindled.