In my examples, i use 14500 size 3.7V Li-Ion Rechargeable Batteries (Brand: TrustFire / Unprotected versions) in my modded Barricades. The batteries can be sourced from specialist electronics stores or online sites.
14500 size 3.7V Li-Ion TrustFire rechargeable batteries are usually charged up to 4.2V, so i use various configurations (along with dummy AA batteries to fill in the empty slots if required).
I know it's been a while since you posted this, but can I ask, where did you get your dummy AA cells? I'm having trouble finding them for a reasonable price.
Also, I assume you are using a hobby charger for the Trustfires, but it sounds like you're using a programmable charger, do you think an auto-peak charger would work with the trustfires?