What would you do?

I would call the highest level person in the company that I could get to and politely explain the situation. Express your disappointment. Then ask how they would recommend fixing the problem. At a minimum I would ask to have a certified repair person install matched drivers in both speakers. And I would ask for them to guarantee in writing that the repair would be as good as factory assembled. That includes using the same solder, wire (if needed), sealing (if any) etc. and that the guarantee still applies. Maybe say you are discussing this will fellow audiophiles on line and this was the suggestion from them. You might find that the company might be much more willing to insure a correct solution than the dealer. Maybe they will even send someone to fix the speakers. I would not let the dealer touch them unless they are an authorized repair shop for the speakers and the company agrees that that is the correct solution.

My guess is that the company does not really want this type of publicity on the web and may well go out of their way to correct the situation. These are clearly not high volume speakers and bad word of mouth could be a real problem for them.

Rok2id seems to have it about right. 50k for a set of damaged speakers. How can you not be incensed?

"the manufacturer forgot to put plastic protectors they normally use to avoid these issues."

Totally agree with Dtc. As the consumer of an expensive high end pair of speakers, you have the right (and you owe it to yourself) to require the manufacturer to make the speakers like new again, whatever it takes. This is the manuf's liability. Unless the dealer is a repair service for the manufacturer, and no matter how simple they say the replacement is, you should not settle for anything but the highest quality solution for your new $50k speakers. It get's my blood boiling a little when I hear of any phile getting trifled with when big money is on the table. I cannot afford such speakers, but I cannot imagine accepting half-stepping by the manufacturer. They need people like you way too much! Hold their feet to the fire.. They need to handle the repair to your satisfaction.

My neighbor just got a new Ferrari convertable. Here in Arizona it gets hot so during the day he used the top and at night the top went down...all worked well. Yesterday it rained here in the Sonoran dessert and the top poured water onto his matched hide leather seats et al. The dealer used tape to stop the leakage. My neighbor is outraged. I am very happy in my Porsche.

Both speakers, in their entity need to be replaced at no cost to you. The old ones collected at the dealer's expense. The dealer needs to refund to you 15% of the price of the speakers as an accommodation for your lost time and money. Nothing else would be fair.