Unfortunate situation, new owner... What to do??!

That excuse about the exhaust is bulls***, completely and totally. Stock downpipe/testpipe doesn't have a flex section in it, nor does the stock cat back, so why would an aftermarket cat back be different? No exhaust vibration.
 
^ I agree, but if the aftermarket exhaust does not have good rubber isolation hangers and care was not used to make sure it was not touching anything else, it can produce vibration.

I put a reso in the middle of the racepipe section of my catless dp/rp to control drone. When I first installed it, I used muffler clamps in order to orient or "clock" it for that very reason because clearance was tight. Sure enough, when I road tested it under hard acceleration, and the engine rocked on its mounts, the reso did touch a crossmember and vibrated - badly, and that is with a flex joint in both my dp and rp. I loostened the clamps, rotated or "clocked" the reso a few degrees the other way, lock it back down, retested, marked it's alignment, then I had it welded in place. We can't exclude there being a clearance problem under there.

Dealer's opinion, however, is probably is BS, though. Easy enough for the dealer to put the car up on a lift and check that. No excuse.
 
I'm going to order the hanger kit from Torque Solutions when I get a chance, it can't hurt, the rear most hangers are a bit squishy compared to the others. If it persists I'll have to drop the system and re-hang it and possibly weld a flex in. I'm also pulling the spark plugs soon, I have a random miss now and the previously mentioned hesitation at low rpm. I find it possible that the dealer may have re-used my plugs. If that's the case, it would explain my issue. I replaced the upstream sensor before the engine was replaced, I wonder if that has some contamination going on as well, no check engine light or pending codes yet. Mass air is clean and tight, only modifications to the car are installed properly (GHL cat back, K&N drop in filter). Fuel mileage is right around 25mpg, even with extended idling at times. Fluid levels are spot on, no odd smells, nothing. I'll be the first to admit that I'm still learning the car, but I've had several turbo/supercharged cars prior to this one and I've noticed the different quirks of this platform. Thanks for the input so far everyone!
 
From what I've experienced, it's your plugs. I had some major rattling and popping of my engine before and I couldn't figure it out. I spent weeks and weeks trying to figure it out. It turns out, it was the spark plugs. They were opened up to .048 or something like that...I dunno. Or maybe it was it 0.48? I can't remember. I had a friend of mine do it. He said it was damn near double the opening that it should have been. He said it was bad....real bad. But anyways, replaced it with proper stock, gapped plugs....And all is kosher....Check your plugs!!!!! I can't stress that enough!!!!!!
 
I'm pulling the plugs tonight after work so I'll see how they look and check the gap on each of them. Putting Denso ITV20's in. Gapped them to .032". I'd be very angry if the plugs aren't new or gapped correctly after having a new engine installed... But there is the possibility of fouling them during the break in period...??
 
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