2. I have a desk & an improvised nightstand (cardboard box with a few books stacked on top), so I don't quite have the same setup as you. If you look at pictures, the E9 isn't huge. I would guess its 6" long, 4" wide, and 2" tall? If you look at a picture with an E7 docked in it, you should get an idea of the size. From what I've read, the "bugs" improved by the E09k are that the smaller 1/8" headphone jack on the older amp gets some distortion, but the workaround is to just use the 1/4" jack instead, and that the old dock mechanism can wear out. There are also different inputs and outputs on the back, but the tone of the sound is the same for both models.
I don't think you could go wrong with either the E9 (or E09k) or E11 amp, though I can understand if you'd find the E11 more versatile. If you get the L7 LOD for your E7, you could connect it to either amp to power your headphones.