Don't mention it, you saved me with those washers... I will give you a special lens for your laser, if only it works, when i test it.
Anyway, the CR2s are different from Li-Ions.. If i knew this before, i would have included some Zener diodes with your LEDs, instead of regular diodes..
The green batteries can be discharged down to 2V each - 4V total. The LavaDrive would continue working off them untill they were dead. There is no protection circuitry in them, so they would get damaged.
The LEDs are supposed to turn on at 2.7V, which is the lowest safe Li-Ion discharge voltage. You need to add 1.3V to that.. This is a similar problem i had with the prototype device i am using these LEDs in (4x Ni-MH powered)...
Maybe you could find a 1.3-1.7V Zener somewhere? You don't need to drain the batteries completelly either and it's good if you get a little advance warning..
If i can find such a Zener, i will send some to you..
About the size.. I have not yet been able to find similar LEDs anywhere else. And they only come in 5mm. But i usually file them down a bit, either to give it a flat top or make it thinner. I don't know exactly how much space you have in there. I was even considering using these in my tiny laser, but it would prevent the modularity of the design... I am sure you could squeeze it in somehow.. The optical fiber is not a bad idea. There are also some plastics that act like that, and are often used in CD and DVD drives, to transfer the light from an SMD LED on the PCB to the front plate.