Unfortunately, your USB port has died
You've done more than enough tests to diagnose the problem and unfortunately this one is hardware related, not software or firmware. There's no NVRAM setting or SMC control that handles power to the USB (directly).
The "light" that you are seeing on your USB device doesn't mean it's connected and recognized by the computer. It simply means it is receiving power on the +5V pin of the USB port.
Looking at the pinouts of a USB 2.0 Port, we can see that there is a dedicated +5V for power (why your phone charges) and two pins for Data (Data+/- for positive/negative voltage signals) and a ground. Data isn't being transmitted (which is why your iTunes doesn't recognize your phone).
What could the problem be?
- It could be a failed USB controller (SMSC USB25138)
- Broken or corroded solder pads/joints on the USB ports or related components
- Physically broken USB port
Any/all of these would contribute to the weird behavior you are seeing.
From iFixit.com, we can see that the board layout as follows:
The good news is that this can be fixed. It's not a DIY type of repair, but there are shops that specialize in component level repairs. Just do a search for "MacBook Logic board repair" (Rossman in NYC is really good - not affiliated, just a happy happy client)
Since you indicated it was only one USB port, the chances are good it's just a bad connection with the physical port itself. An immediate fix would be to purchase a USB Hub (powered preferably) so you can get your connectivity back.
So lets see if I have this right... if you shut it down it turns back on no problem. If it goes to sleep it takes 5 days to turn back on.
Just a suggestion... what if you turn off sleep in System Preferences -> Energy Saver? I'm interested if it does the same thing if it stays on but just goes dead.
I would also try a fresh OS install either from a thumb drive or internet recovery in case something in the OS is causing the issue. It's easy and you can reproduce the issue quickly so its something to cross off the list pretty fast.
I assume you tried the obvious SMC, PRAM resets, etc... SMC controls a lot of the hardware so that's the one I would think is most likely.
Once I had a MacBook that had a bad thermal sensor. It would turn itself off and take a few hours to turn back on but that was pretty obvious that it was hot and overheating so I would assume that is not the case here. If it is getting hot then keep that in mind. Also the MacStore replaced the motherboard and that did not fix the issue so they replaced the whole laptop. I am not sure what the actual fix would have been.
CleanMyMac has thermal warnings that can tell you if its overheating. This may also tell you if you have a bad thermal sensor. If you just turned it on and it's reading 100c then there is something wrong.
Let us know if it may be overheating or if just plain going dead works and it's only sleep mode that does this.
Edit: This stood out in an article about overheating...
- Fake MacBook Charger
A normal charger for a MacBook Pro includes three main parts: AC power cord, MagSafe Power Adapter, and MagSafe connector. It’s always good practice to use the original ones that came with your Mac. If you bought one online, it could be fake and might not work well with your MacBook Pro, thereby causing overheating problem and other issues.
How to Fix It: Shop from the Apple Online Store or Local Retailers.
It’s often not so easy to spot a fake MacBook charger, but this YouTube video shares a few awesome tips. Check it out. Also, try to avoid shopping from online marketplaces, other than the official store, for Apple components. Don’t be lured in by lower prices. I can’t stress this enough.
Best Answer
I youtubed/googled the issue and all I needed to do was remove the battery plug on the logicboard and I guess the system resets and it worked again. MacBook Pro alive.
How did I learn this? This happened to me at well. I had my MacBook Pro 17' connected to my Thunderbolt Display and when decided to charge my ipad using the USB and when I connected the iPad, everything shutdown. I couldn't even power it back on. Took it to apple store and they told me 500 bucks. WHAT$$$ They don't even diagnose the problem.