It's the wrong battery mate. The reason the bike won't crank over with the battery fully charged is because its ampage is too low. The correct motobatt battery is a MBT14B4. Your battery has only 9amps when it should have 14 amps.
Take it for a long ride (an hour +) with it installed properly and see how it does. I've kmackered a few batteries with mains chargers in the past and don't really trust them personally. Motobatt are normally tough as granite, so with a bit of luck it'll recover!
I may be talking out of my arse here but I have read somewhere that these motobatt batteries don't like to be deep cycled (allowed to go completely flat), they will look like they are taking a charge but won't have the amps to start. You could try giving it a jolt from a 12V car battery to see if that wakes it up then give it a charge. You may just have a defective battery and if it was me I would fit a new one before going away.
I'm not up to speed on gen 2's but i think it should be fitted as manual states and how it was originally fitted. It sounds as though it needs a good charge from a car charger to shake it into life. I also have an optimate and they can sometimes be a bit of a pain, when trying to get a flat battery back to life. I wish you luck!
I have never seen a battery on a car or bike installed sideon? Always terminals upright.Am I missing something?I have a motobatt on my gen 1, no problems fitting apart from the way the terminal posts bolt on made attaching leads a little awkward.