If I leave without an extension it's going to look like I was here illegally for 5 or so months. What should I do? Are Immigration gonna be pissed? I don't want to cause trouble.. this has been relatively smooth sailing so far (long journey though)
Thanks for any advice
You will have no problem when you return (with all your paperwork) to land.
Even if they send you a rejection letter for the extension, it wont matter, you are very likely to have landed anyway.
Either way, extension or not, they will know were you are when you land

It happens to a lot of folk.