It always helps when you know what the mats are used for, so you can stack them in quantities wich fit the craft. When you need 5 logs to make 1 lumber then it makes sense to sell the logs in stacks of 5, 10, 15, 20, 25... for example. This way the crafter has not to buy something extra wich he has no use for, when there are only stacks with 6 for example. On the other hand you can make him buy that one more than he needs...

In general I sell stuff in smaller stacks of 5 or 10 items or one by one. I have to refill the retainers more often, but I have the impression that stuff sells quicker.

I would avoid Ishgard, all the other markets are fine. Limsa is maybe the best option to sell stuff, but it depends on the server how active every city is. Ishgard is not that active, there is also only 1 market board in and no housing districts, wich means there are not many people who will buy from Ishgard. Ul'dah is maybe a bad choice too, not many people like the housing district so a lot of houses are maybe only placeholders for relocation and not many people actually hang out there.

But overall people seem to have no idea how the taxes work. They will rather buy the item on top of the list to safe 10 gil and pay 1000 gil taxes than buying for 10 gil more without taxes...

Making 1 mio gil per day should be possible with not too much work.