What would be the best way to connect the reservoir to the river without flooding? Should I automate it with pressure plates or should I go with levers? Will fortifications in the aqueduct protect the fort from carp? Are doors or floodgates better for water control?
Fortification won't protect from swimming creatures once water in it is 7/7, it doesn't stop things from being pushed in from flow either. You can pump water through floor grates, though, which does stop creatures from coming in. I don't think it protects from projectiles, though.
If you want just simple and basic water control, then having diagonal only opening will depressurize water. If you want something more complicated, then pressure plates will do the job. Personally prefer using bridges whenever possible if I have to seal things off, partially because bridges will smash anything on it, otherwise doors works because it's faster to close than floodgate.
http://dwarffortresswiki.org/index.php/Pressure can help you to figure out how to not flood yourself, though.
As for rest of your plan, pump draws water from the z below it at it's intake. Water pressure tries to go to same Z as pump's exhaust ( which's on same Z the pump is ) unless it goes through diagonals, which resets it's pressure. I can't really say if your plan and ideas would work out, but I can say if you're not in a rush to pump water up, then dwarven power's okay for it. Well, as long as the pump's working end isn't submerged, you'll need power to drive those.
Your main design concern will be making sure the waterways are sealed properly, hopefully walling up any holes instead of using door for accident-prone dwarves to trip into water itself. Pumping's better done by power, but if you have plenty of dwarves exercising, and doesn't expect or need much hauling, it'll work as long as there're only 2/3 or 3/4 as many pumps as avaliable dwarves, or you're willing to micromanage turning them on and off.