If I were to attempt building these little "ships in a bottle", I woudn't try to modify the existing bulbs. It's very difficult to get these apart without destroying the mounting sleeve and/or the annular glass insulation around the bottom contact. I would start with new components.
Empty BA9s bases are available relatively cheap. For constructability, I might try soldering a couple of segments of thin magnet wire into the base leaving about a 1/2" portion sticking out of the base. The LED/resistor/diode assembly could be built separately "out of the bottle", then soldered to the exposed magnet wire ends. Then the entire LED assembly could be simply inserted and hot glued into the base. I think there is plenty of room to work with to install both the diode and resistor in the 8 to 10 mm space available.
