haha! ouch....
i never commented on a couple of the points earlier... op, you mentioned the floor getting hot... i like to think i'm a car guy... what do you think caused it to get hot? i can't think of what would do that... exhaust is the only thing under the floorboards and it is already hot as sh!t normally... maybe you'd feel heat through the firewall, but that it not the floor...
transmission shouldn't be affected at all. not to say you aren't feeling something that you might think is transmission... is it the cvt or manual?
as for comments earlier about the new engine not affecting value... maybe not considering it is so new... but usually yes.. and let's be honest... ANY flag brings down the vlaue of a trade in.. valid reason or not. if you were buying a used car and two were priced the same, one that had to have a new engine put in it at 8000km(guessing) and one that is factory, would the choice just come down to a coin flip? personally, i wouldn't take the new engine one unless there was a price drop.