Without knowing what the problem is, we can’t advise driving the vehicle any farther as you risk doing more damage. Clearly there’s something with the driveline and the car needs to be scanned to find out what it is.

On the plus side, often the blinking D indicator light means there’s a problem with the transmission pressure sensor, rather than a major problem inside the transmission itself. But until you can determine that for certain, driving the car at all is risking destroying something large and expensive.

Your only course of action at this stage is to pursue Honda until the company does what it has said it would do. But for backup in case things don't go according to plan keep careful records of every discussion you have with your dealer/Honda so you have all of the relevant information about your dealings on the problem to use as ammunition should things go sour. At the end of the day you could resort to the laws relating to consumer affairs to push your case, and the more information you have supporting your case the better.

All cars today are fitted with air-conditioning and there's an assumption that owners will use it, and use it all the time regardless of the outside temperature. As a result there is less emphasis placed on making sure the ventilation system is effective for those few people who prefer to get their air that way. The air coming through the air-conditioning system is as fresh as that coming through the ventilation system if you switch the a/c over to outside air, and if you set the temperature to around the ambient the load of the system won't be overly high and won't affect your fuel economy too much. Other than that there's not much you can do.