What time should I arrive at Big Sight?
If you wanted the best chance to get rare stuff, I'd say 6-7 am. If you just wanted to look around and don't want to wait in lines, 11 am.
How should I prepare before going there?
Bring at least two water bottles and food/snacks (though there will be vending machines and convenience stores there, you'll have to fight those lines as well). Towel might be a good idea, as well as a spare bag or two.
How long are the lines for the popular stuff? (eg LoLK)
ZUN's lines go fast since he's only selling the one new thing each event, so while it may look long it shouldn't take too long. Otherwise, any door or popular wall circle could take up to two hours or so.
I'm interested in Renko/Merry/Hifuu Club stuff, what would you people recommend?
They group circles by what characters they feature, so if you find one Sealing Club circle, you should find the rest very close by.
I can't read/speak Japanese well (only know really basic terms), so is there anything I should take note of?
They will sometimes split up very long lines for better management, and at the end of each chunk of line there will be someone holding up a sign, either saying "最後列 (end of line)" or something else that means "line portion" if you just remember 最後列 you can tell if its the end of a line or not.
How difficult is it to navigate through the area?
If you mean trying to find stuff, it's not too hard. If you mean trying to walk through the crowd, it's a lot more troublesome. However, I recommend taking the rear path between East and West Halls since it's much faster. It should be located on the map.
I'll also be in Akiba for a day or two, so where can I find cheap-ish Touhou figurines/artbooks/doujins ?
If by cheapish you mean second-hand, K-Books, Mandarake, and Lashinbang will have a lot of stuff.