On point two, people are fine with a single currency. In fact, its often been asked to please stop introducing new currencies. Commendations of valor, tokens of the 12, call it what you want, if it behaves the same then its the same. In this case, it does not behave the same. Tokens dropped at the end of every quest and were bta. Commendations of valor are btc and only at chain completion. I'm fine if you want to make tokens at the end of a saga only, but at least make them bta.
On point two, part 2. There will always be people that can do in a few hours what takes people days to do. This system will just make it so that there will be people that can do in a few days what others can do in months. I would seriously suggest not trying to make adjustments to beat the outliers.
On point three. You are not just depreciating tokens of the 12, you're depreciating entire swathes of Eberron content. Make more sagas and have those apply to a broader range of quests. Because otherwise this seems like a shot in the foot that turns people off altogether. I get that you see a lot of people already have older content and want to motivate them to buy new content. Adjust the xp and loot systems to be both comparable and stable, and people will buy new content. Completely invalidating previous content depreciates player confidence in the game, reduces the variety of things to do, and in the end may very well serve to have people stop buying content altogether when they move on to another game.