2.) suck air in carbon fitler -> 6" vortex -> out the window
suck room cool air -> 6" vortex -> 2k watt -> out the window

I'd go with plan 2.) but use an 8" for the cooltubes. I use a 6" for a 400w and it could cool two but for 2 1000w I'd feel a little better with a bigger one. If you dont need all the power or want to quiet it down some, get one of those speed controllers for fans.

At one time I considered doing what you planned in 1.) but several of the people here thought it was not a good idea to draw through the carbon filter first, then over the lights so I ended up with two fans.