One idea is to get a different cheap stick and tear out the stock parts and put in your parts (and do the wiring to the PCB/put in a PCB you buy)... if you want to get something for 50ish. I did it with the mayflash universal PS2 stick (and it took a lot of effort, soldering, etc. It's basically modding the stick with better parts.). If you're going down that path though, I'd say find a Madkatz SE that you can mod instead... it seems easier from what I've looked into.
As for actual cases, Foe Hammer has DIY cases, but they're probably the expensive ones you saw (85 for minimum diy case, and that doesn't include shipping), art's hobbies acrylic arcade sticks for slightly over 50 (http://www.tek-innovations.com/arthobbies/?loc=products&cat=12). If you want some more ideas, I'd check Shoryuken's Tech Talk. There are people that have even used a tupperware container for their stick before.