I would do one or two things differently -
First, rather than soldering to that many LEDs I would probably prefer to solder to snappable pin sockets, and then plug the LEDs into those. That way if I screw up a polarity (it happens!) or whatever, I can swap the LED easily.
Second, instead of using individual resistors I'd probably look into multi-resistor packages. You can get DIP-packaged resistor networks (multiple resistors tied to a single line, for instance, or just a bunch of resistors in parallel if you prefer - the disadvantage in the former case is that you need to run two lines to each LED rather than one line and a common ground - but I think running two lines would be simpler anyway, don't have a mess of ground wire everywhere.) - you save a bit of board space compared to mounting individual resistors on a board (doesn't sound like you were mounting the resistors on a board anyway) and if the resistor package ties to a single line then you also save soldering work.
Third, the risk of a short circuit between or across LED lines can be mitigated somewhat by having the resistors be "upstream", as close to the voltage source as possible. That way if there's a short anywhere between where the resistor is and where the LED is, the voltage will still have to cross the resistor before reaching the short, so the LED won't light but most likely nothing will burn out, either.