Just to make sure : I guess you did know that the choke can be pointed in any direction that you please ?
Just a thought... I replaced the OEM carb with a brand new one on my 2010 Agility today, and I had to turn the choke 90 degrees to make it fit under the seat, just like I had to do with the new one on my other Agility... Those carbs all seem to be factory-assembled with the choke pointing sideways, which doesn't fit under the seat...