It's a long post but I feel it will be the best advice, so spear the 5 minutes to read it(I'm saying this cause I really feel for you)
hey, man I saw this thread by accident and I feel for you.
You don't have to worry about this whole thing It's a must in every good relationship, to have a fight or something dramatic like that. It only strengthens your feelings. As you said now she knows you're willing to walk away, and won't take you for granted - she'll appreciate you more. (it like with drug/alcohol/smoking addictions at first you start and at some point when you feel the withdraw it only stengthens your addiction)
Btw i loved that you cried with her - it amazing! You can't imagine how gold this is.
As for you two meeting I'll share in my experience what you should consider:
Tell her that you want to have a talk, without fighting, no blaming,etc just sharing feelings. Tell her that you have 30minutes/1hour (you choose how much) like a sharing bouble - you can say anything, share your feelings AND nothing will be used against you or her.
it's better to do it tonight, so just tell her that tonight she can come to your place and just talk it through, tell her this is the only way you can see it work out. It will also give her s few hours to put her in the right state of mind(she maybe has other things on her mind now, etc), keep this meeting short and a little bit cold(a little bit, don't be rude or try to hurt her), but tell her that you can't wait for tonight.
as for the night when she comes set the mood - dimmer lights(or maybe candles) have some food
just remember not to over do it, but you have to set a mood since you'll be sharing your most inner feelings and thoughts
after you've eaten, maybe talked about something, maybe played some music and danced together it's time to talk.
You'll know it the right time when you basically cuddle up to each other - she snuggles in your arms and puts her hear on your chest/showders
reasure her again that you can and should say everything you feel/thing/have done/will do/ how something has made you feel AND NOTHING WILL BE USED AGAINST EITHER OF YOU! And there will be no interruptions when one is speaking. You're goal is to share not to argue, not to fight, not to fix anything, not to resolve issues. Your goal is to share!
As for what to talk about:
Don't leave anything unresolved, and tell her that you shouldn't leave anything unresolved.
Now it't time for some AFC

(I know we are all PUAs but if you want a loving relationship there is time for AFCing)
about the facebook things - tell her how they make you feel:
that you not having pictures together and not having the relationship status up makes you feel like she doesn't like people seeing that you are together and as if she's ashamed of you/being with you. (Remember no finger pointing, no accusing that she's bad - it's just how it makes you feel)
as for why you haven't asked her to have pictures together/change your relationship status - tell her that you respect her and her personal space and don't want to make her have pictures with you or change her relationship status.
Now let her tell you her side of the story - how she feels, shy she din't
You just listen and be present in the moment, don't argue, point fingers etc. just listen and (try to) understand
About the ex:
just tell her how it makes you feel (for the 10th time - no arguing or finger pointing) tell her that you care for her really much (or say the big L word if you'd like) and wouldn't want to lose her like that (Yeah I know it's AFC and insecure BUT guess what you are insecure about that, and if she wanted someone with no feeling she'd be dating and Ipad). Tell her that you feel like he's trying to take advantage of her (the thing about the quickie) and that he may be doing everything he is just to sleep with her (AMOG destroyer, every time he does sth. she'll at least consider that he's just trying to sleep with her), that he may be not be over her.
Also tell her you that you trust her and respect her, but she that also that she's the only girl that makes you feel like this and it's hard to fight feelings
Tell her that you thought what you thought: that they are seeing each other behind your back etc. tell her you can't help it and it's not that you don't trust her but rather that you don't want him to do something to her.
Who knows what kind of person he rally is. Maybe he wants to sleep with her so bad that he's willing to get her drunk, drug her, rape her etc.
Just do say that he's that kind of a guy(she may start to defend him) just say that those are some of the thing that went though your mind and you worry for her(you have feeling for her after all, who wouldn't worry..).
Say what's on you mind and how it made you feel (Remember it about how it made/makes you feel) and again no pointing fingers just sharing feelings.
Let her tell you her side of the story, how she feels
It's important in a relationship to see things from your partners perspective.
And keep going if there is sth. else you or her wants to share.
Cuddle together, cry together, feel connected
This is a natural phase of successful relationships - seeing things from each others eyes, sharing most inner/deep thought feelings, no sugar-coating
After this things will be great, you'll love each other more, appreciate each other more, etc.
(as for the ex either she'll stop communicating with him on her own(don't force her) or if she still want to keep in touch tell her that you'd like to meet him one on one, you and him and idk - play xbox, go for a drink, play pool. you want to make friends with him, make him like you and not see you as an enemy but as someone who's better for his ex girl, she'll love the maturity, OR if she doesn't like the idea don't push it. if she says it's not a good idea- just reply "ok dear/hunny")
Just don't dwell on it afterwards, keep it cool don't mention the talk you've had if she doesn't.
The important thing is that she now knows how you feel and how what she does make you feel and you know how she feels and how what you do makes her feel.
Last word of advice: make this "sharing bouble" a regular thing - once a month, once a week you do that