Always useful to take just a few minutes with an Excel spreadsheet, type a short list of your wire/terminal connections, print them out and then cut-- so as to have a bunch of little 'flag labels' you can put on with masking tape. Saves a lot of time later-- and also, something in the process 'I' have learned (and realized I had here forgotten), if you have already determined the pin out from your peripheral to your MCU (pre-planning, in the long run, is never a bad thing, less otherwise you suddenly realize you are 'out' of suitable pins), not only put the peripheral connection on the label, but also (as in this case, for the Teensy 3.1) the respective 'connector' pin you have designated.
For one, if you ever for some reason have to take the assembly apart, it can then be quickly 'reassembled'. And though I know there are much more 'brilliant' minds out there than mine, many times I see even this breadboard builds, which are beautiful, but nothing is labeled, which I think makes 'systematic troubleshooting' just that much more difficult.
One last point, the BPS style wire headers are not only really convenient, but also cheap enough for the price. While not quite as excellent as full 'custom crimp' connector, if you are building a 'single fixed project', a little bit of superglue placed between the plastic sides of leading headers, inserting them one at a time, and letting it cure... You have a decently stable, low cost cable assembly.
In addition, I plan on adding heat shrink wrap once the design is finalized.