Long list of "software" problems on iphone 4.

My wife and I have iphone 4s, purchased about a year apart (I got mine as a cheaper leftover after the 4S came out.) My phone is fine but hers is having a long list of weird problems nothing seems to permanently fix. It is about 2 1/2 years old, and covered under a product replacement plan from Future Shop, where we got it. (Our city just got it's first Apple Store over the holidays.)
The problem is all of her issues seem to be software or "network" related, yet all the common fixes/tests are not yielding any results.
The biggest issue with the phone is with iMessage. I know it is normal for the occasional iMessage to send as an SMS instead, especially if there is a hiccup in the network. The thing is, hers does this all the time, sometimes mid-conversation. If I send her 3 messages in quick succession, she might get #1 and #3 as iMessages but #2 wont appear until 15 minutes later as a text message--making trying to converse via message really annoying. It has done this for several months now, getting progressively worse. We have 3 friends who are our neighbors in our apartment building. We can send a group iMessage to everyone, everyone will get it as an iMessage, but she will get it as a text, usually anywhere from 10-20 minutes later. One of our friends can't even send her an iMessage--he will only ever get the green "send as text" option for the send button, even if they are in the same room, and connected to the same wireless network. When another friend in the same apartment tries to iMessage her from her iMac, it tells her "that is not a valid number for iMessage"--yet it clearly is, because iMessage DOES work...sometimes. All 5 of us are on the same network, Virgin Mobile, so it is not the network--none of us have any problems except for her. It is frustrating because during the day we are both at work and don't have coinciding breaks and sometimes I NEED her to get a message, and it is bad now to the point where I can't be guaranteed she got my message until I get a response back later on. We have not tried turning "send as SMS" off yet, because we don't mind the phone sending an iMessage as a text when iMessage is not available--what the problem is is the delay, the likelihood she may never even *get* the message, (sometimes it doesn't send at all.) and the fact that it will still do this even on a strong full signal or wifi (the wifi network in our apartment is fine, our computers, xbox, 3DS's and my phone never have any issues.) We can try it, but my worry is that if something is wrong with iMessage, turning off SMS will mean she'll never get some of these at all. (more often than this happens as it is, mind you)
Her safari is also extremely laggy, which seems to hint at a connection problem, maybe.
The phone has been reset 3 times. Once, we reset it and restored from backup. No dice. Then, future shop reset it from the phone itself while they had it over night trying to duplicate the issue. Still no dice. Finally, on the advice of a future shop tech, who said they can't do anything unless we can prove a hardware failure of some kind, advised resetting from itunes and NOT restoring from backup. So we did that--the phone was completely reset as "new phone", and nothing has been restored from backup, only contacts from iCloud. Right now the phone has only 2 apps re-downloaded on it, and a few songs, and it did it again earlier today. So, still no luck. (It hopefully goes without saying we have verified all her software updates are done and everything is fully up to date.)
After the reset, a new issue surfaced--it was vibrating randomly. After troubleshooting, we discovered she was getting vibrate alerts from email, despite the fact that email push notifications are OFF and her email app was closed at the time. She had to turn off vibration and sound for email to get it to stop. Now, maybe that is what she has to do, but my iphone has push notifications off as well--but sound and vibrate still on--but will only beep/vibrate if the mail app is open. Otherwise, I don't get the notification. (Maybe my phone is broken, and hers is doing what it should for once? LOL) The thing is, she never touched that setting the first time she got the phone, and has NEVER received vibrate alerts for email. Why suddenly after a full reset would things be enabled that were never on in the first place?
So I am stumped. It is a huge inconvenience to keep resetting this stupid thing, and we don't really want to pay the genius bar to look at it, but I can't help but feel like these recurring problems can't be software related when we've had this reset so many times--and it's not "network" issues because she is the only one. We have tried checking the diagnostic record for panic.plist (wishful thinking I guess), read through a ton of posts here, and tried what we could... any further advice/what we can try? Is there any chance this IS hardware, something corrupt in the phone memory/storage? An issue with the receiver? If so, how do we prove it? Can the genius bar scan it somehow?

If you have an Apple Store in town, setup a genius bar appointment.  The genius bar tech should look at the phone and try to diagnose the problem free of charge.  They may not want to fix it free of charge, but they should perform their diagnosis and tell you what they find for free.
It sounds to me like her iPhone is losing its connection to the Apple iMessage servers.  You might try actually turning off iMessage snd signing out of iCloud on her iPhone, then after a restart of the iPhone sign back into iCloud, then turn iMessage back on.  There is no guarnatee that this will resolve her problems, but it might help.  If her iPhone is not connected to external power, and it has been more than 10-15 minutes since she last used it, it has probably turned off the wifi radio, and will be depending upon cellular data for the iMessage traffic to flow.  This could easily account for the delays she is seeing, and even it dropping back to SMS, especially if you have poor cellular data coverage.  If this is the case, then getting something like a Mophie Juice Pack Air for her iPhone might help, as it would allow her iPhone to be connected to external power (the Juice Pack) thus keepig the wifi radio on more.

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