The pump will fit behind the rad rather than next to it (no space), it won't impact on airflow sufficiently to notice. The res tubing can drop virtually straight down to the pump inlet depending on pump orientation. With an pump top you could use a side outlet to the rad.
You may a find a tall res a bit of a squeeze due to the cabling on the 24 pin motherboard power connector unless you drill the tray and come up from behind (as the actress said to the bishop). I use an EK Multioption Rev.2 100 which is about right and use a pre-drilled hole in the motherboard tray which may not be in the correct position if the motherboard tray is reversed. Move it over too far and it impacts on the hard/optical drives cabling.
I'm using 3/8"ID, 1/2"OD tubing mainly because I found it easier to route and now I've finally got some decent tubing don't get kinks or need to use anti kink coils. I got some samples of the different sizes of tubing before I put it together. I'd also read Cathar's tests and decided the differences were too little to matter.