3 minutes is a bit short. It could be that the battery is getting weak, but it could also mean the there is a bit more energy required to make everything work. If the motors strain a bit more than when it was new, perhaps it causes the batteries to last a little less time. You could disassemble, clean and look for any bent parts.

I have bought a few batteries for my MCX and MSR from HobbyKing. The 160mah from Turnigy works fine, but the 138mah from Flightmax didn't work for me. Watch our for shipping cost. Might not be worth it for you unless you need something else.

As far as the flybar goes, as long as the whole thing is balanced, you might have a bit more challenge to control the heli, but it shouldn't cause anything bad to happen.