When troubleshooting, I always start simple and then work my way up from there.
You said the bike had been sitting for a few days, causing the battery to die? IMHO, your battery shouldn't die in that short a period of time. You'd be surprised how many problems can be caused by a weak or dying battery, so I'd start there.
Is is possible your bike may have been sitting longer than a few days? If so, it could be a fuel problem....you may have gotten bad gas. OR, if you filled up with fuel containing ETHANOL, after a few days of sitting, the fuel and the ethanol will separate, which could have caused your problem. Topping the bike off with fresh fuel may have alleviated this.
So, I'd tackle your problem in this order:
1. Replace Battery and check all connections for looseness or corrosion.
2. Run a new tank of fuel, adding a carb cleaner like Seafoam in it.
3. Investigate fuel pump and replace if necessary.