Looking at the ecigmods website I can't see what the difference between the "5V" and "6V" passthrough is.

It's unregulated so whatever voltage source you use will give you that voltage. Right or wrong, anyone??? You should be able to use a 5V/2A adapter with no problems.
You say you are using a 5V battery in your mod. Is this the NiMH battery? This '5V' battery is actually 4 600mAh NiMH batteries in one 'package'.
Check out the Puck mod (link in my signature). You can put this together for under $10 (not including the price of NiMH rechargeable batteries that you can buy locally). I've been using Puck-style PVs (I use a 510 connection) for months and the batteries (1000mAh AAAs) last me more than 10 hours. Others have used AA (>2000mAh) NiMH batteries and report battery life as 1+ day(s).