1. When does EK make D class seats available? Is it 11 months before? 5 months? 3 months? Or they do it in batches?
There's no real consistency, it can be any time, or never.
2. The cash paid in addition to the miles when issuing an Award ticket: is it the taxes and government charges or is it "padded" with other fees and charges?
There is the carrier imposed surcharge on top of government taxes. This differs depending on the market.
3. When offered an upgrade on the spot upon check in or when boarding: is the number of miles deducted equivalent to the Saver Award? The Flex+ Award? different.
It's the same as would be if you'd booked it online.