Make a custom plastic case
If you're only making one it's entirely reasonable to just order a plastic project enclosure (all sizes are available) and then drill and cut holes yourself. 

 

The issue it seems you're trying to overcome is a lack of craftsmanship, you can help alleviate that problem by purchasing the correct tools for the job. The other keys are practice and patience. Literally measure twice, cut once.

For instance you can buy some corner punches for cutting out nice square holes. These ones, for about $30, will fit in to a small drill press (just for the press portion), which you can get for about $130. For drilling precision I use a cross-slide vice mounted to my drill press. This improves the linearity of the holes I drill significantly. 

 
 

So, get yourself some of the right tools and the quality of the project cases you build will be much better. You'll also only pay ~$10 for a case rather than a couple hundred for a one-off. 

Labeling can be easily achieved by printing a large stick on label (or paper, like this guy image below) that you can cut holes in using the case you've already made. 

 

You can also order some custom stickers with common symbols/markings. Or simply order the case with labels/markings printed directly on to it.



3D printing is a good option too, but is also a lot of design work for a single case.

Take your time, you'll end up making some very quality enclosures that you can be proud of for years to come.