I know that the last chapter is weird as carrot pancakes, and there's a lot of unanswered questions, namely these:
What has Clary done to get the fire inside her in the first place?
Now the statue of Raziel is not everything that it seems to be, so it IS the runes she read out loud that did that to her, as well as something else within the statue.
Why did Clary test herself with the runes in the book, that she knew were dangerous?
Remember that Clary didn't actually use the dangerous runes. She just didn't realise the power of so many runes at once (she is actually new to this world, remember)
Who wrote the book?
Well hey - cliffhangers.
If Clary is a professional fighter, why is she so bad now?
Clary still is a professional combat fighter, but Shadowhunter is very different. In this, she's learning how to kill things - anyone who's done any kind of martial art or fencing etc. will know that you don't actually learn how to specifically kill anyone, just to defend yourself.
As a child, did Valentine put angel blood in Clary?
I'm going with yes on this one.
If they know Clary's a Shadowhunter, why haven't they got HER memories back?
She never had any blocked memories (in this version at least). Jocelyn just never told her about any of it. It was only the Lightwoods that got their memories fuzzed out.
Wtf is up with Clary?
I know she's insane right now, but this is the only insanity I'm planning. I was having fun playing around with the dark side of the Marks, but now that Isabelle found her, I think that's good for now.

I cut the chapter in half because it was so long, so bear with me, please. I know things have got a little bit out of control but please please please stick around because I know what I'm doing :)