I still haven't seen how and why you need an Arduino. All you've done so far can be done with a NE555 for a lot less money and a lot less effort. That is not to mention that the entire 555 circuit can be enclosed in one of those tubes/rods/candles/whatever.
Take some time to study the NE555 and you'll see that it might fit your needs a lot better than the Arduino, specially when comparing costs.
The idea is to have 6 LEDs; red orange yellow green cyan blue. It's arguable that only red green blue are needed to make up any color in the spectrum. However, orange yellow cyan are pure wavelengths of that color.
Each LED is independantly controled to do pretty much anything you wish them to do. Such as flicker like a candle, flicker like a guttering lamp, flash, fade in and out, be of a particular colour, and have variation in brightness. Or have it set as colour temperature adjustable, so that it only puts out light where the spectrum is weakest.
The device is to be capable of being upgradable, for example, for receiving IR data from a remote control, or being triggered by a laser pointer. It is not intended in its pre upgraded form to produce a dazzling light. It's purpose is to replace ordinary candles. For example, you might keep a candle in a garden shed. Well you could keep this electric candle in the garden shed instead, reduced fire hazard. When you enter the shed or attic or cellar / place with no light or mains supply, you just point your keyring laser at it and on it comes. This means you don't have to stumble over piles of junk in the dark and risk injury in order to get to the far end shelf where the candle would traditionaly be.
So, depending on your requirements you need to choose what sketch is to be downloaded to the candle.
Now, I can think of dozens of permutations, applications and uses that this candle could be put to. However, I don't want to have to keep redesigning brand new enclosures every time a new upgrade comes along. And I want it to be backward compatible with the battery box, and other modules.
Supposing a new LED comes out that's an improvement on what's around today. I don't want to build a brand new system. I want to be able to pull out the LED module and replace it with the new, leaving everything else untouched.
I am still not exactly sure what your question is, what you want help/collaboration on.
So having provided a bit more back ground into the whys of the project, the scale of its ambition probably becomes more apparent.
The vision is to produce an open source enclosure construction system which is easy to assemble / dissasemble and looks aestheticaly pleasing. Provides robust build and is cheap.
This means, that everyone is free to take the construction blueprints and manufacture on a scale in their own community. To make it work however, there needs to be some agreed upon standards. For example, I have chosen a 50mm diameter for this project, but other projects may require smaller or larger diameters.
Current available off the peg enclosures are a real pest for tinkerers and often look shabby, unless you put lots of work into them.
So how is a thing like this built?
Help on applying the Open source GPL to its constuent parts.
Help on working out the threadings to be used.
Think of it like an open source software project except here the software will be gerber files, CNC milling files, dimension measurements and legible building instructions, as well as numerous sketches to run the product. The more people involved in creating this product, the better it will be. And we can find cheaper and cheaper ways to produce it, and at the same time be offering a GPL, perhaps the first GPL product aside from Arduino, the first GPL product for domestic purchase.
In the meantime I guess I'll just keep posting what I have come up with so far. I hope this helps. Thanks for your interest.