Its been a while since I've played, so I'll answer the best I can.

1 - The tax levels can be raised in each area to gain additional income at the cost of pissing off the local populace and having to re-do the mission once they rebel against you. Funding is used for gaining new weapons and gear, if you pick up a new item during a mission, the first you can find being an Uzi, it will be listed in your research page in place of "automatic weapons". That way you know what your getting when you research a gun, otherwise you won't know what your next auto weapon you'll earn will be (unless your familiar with the game). Research funding can be increased to reduce the time spent on research... I think, in the long run its the same price though. I can't remember the rate your income comes in at... I think its daily, but initially research will cost more than your income rate until you manage to grab a few areas.

2 - Only running costs is research costs and the price to buy ammo, including after any failed missions. Agents die permanently so there's the loss of the costs for bio-parts to remember.

3 - Ingame time does effect the global time, I'm pretty sure that mission time is accelerated compared to global. I think that nothing changes while you are in any screens outside of mission play, its only after a mission is finished that changes are made to the world (rebellions started etc, rival syndicates take over different areas). The game does get harder as you progress but I'm pretty sure its map based.

4 - Missions is exactly the same as before.

5 - Nope, you pretty much hit the nail on the head with how that works :)

6 - Honestly haven't got a clue, I always thought the funding research was its daily cost.
After a little thought I think the thing is: you make several payments a day. The progress bar has several increments during each day and that you pay as each increment is completed.

7 - Don't know that either, I also go with the "next level is better" thing.