Control charger with NPN-Transistor

I'm trying to control a higher voltage power source with my arduino and general purpose NPN-transistors but I am getting nowhere.

I've got the charging circuit from here; http://www.i-hacked.com/content/view/207/44/'

And I don't need the "Don't charge those batteries"-speech, I know the risks involved.

My arduino is monitoring the voltage on the battery as it is charging, and i would like to use the arduino to cut the power when the voltage has reached a specific value. How would I implement a transistor switch, base-controlled by the arduino, into this circuit?

Ordering a couple of relays now, might as well use those.

It's difficult to figure out why your design with npn failed, as you didn't provide schematic. But I will advise to look at: http://ruggedcircuits.com/html/circuit__11.html

Or http://ruggedcircuits.com/html/circuit__17.html It provide 3.3V , that exactly what you need for 2 AA, so you 'd not need disconnect them at all, just keep under trickle charging current that drops to low level after batteries get charged.

That circuit is best controlled with a PNP transistor to do high-side switching before the regulator. However you'll need an NPN to shift logic levels up to whatever Vin is.

There is probably a much better way to control that constant current circuit directly at the sense terminal of the regulator.

I haven't got any pnp, and there's a 2day delivery time on any parts, are there any negative sides to using a relay, or is it a viable solution?

Yes a relay is perfectly viable, remember to include a reverse biased diode across the coil and drive it with a transistor.