The only option you are missing is the Kobo Aura, not to be confused with the Kobo Aura HD (which has a slightly bigger screen, 6.8" compared to the rest being 6", and is consequently the most expensive). If you preferably want $150 or lower, you are looking at the Kobo Aura, Kindle Paperwhite and the new Nook Glowlight. I'd dismiss the Kobo Glo just because its and older model and the screen & lighting should be improved on the newer Aura, but you might still want to consider it, it'll certainly be cheaper.
Plenty of space rules out the Nook (only 500mb and the new version no longer has an SD card), the Paperwhite is ok 1.25GB (only extra is cloud storage), while the Aura definitely wins on space as it has 3GB (and SD card slot for up to 32GB).
On your main consideration, customisation, the Aura also wins, sort of. The Paperwhite is ok, gives you up to 6 fonts at various sizes and a few options for margins, line spacing etc, but not to the same extent as you can do so on the Aura. It has more options and you can also use custom fonts, but that is negated very slightly by the extra space in the header and footer of the page on the Aura (it can be lessened by patching/editing CSS files). Check out the images in
this post in the Kobo forum for some photos that show the Kobo Aura and Glo together, and the last photo shows the Aura and the Paperwhite (and it shows this wasted space particularly in the footer).
Kobo's customer service can be very hit and miss, especially when compared to Amazon, but that apart. it sounds like the Kobo Aura is possibly the best option for you. I'm pretty sure you'd be happy with either of them though.