Prices have changed since the OP made this post. The cost of the franken build has gone up as has the pricing of the used gen.
$5k is on the very, very high end, still. But absolute dollar amount of franken vs gen is still the way to look at it. The gen is going to be $9k to $10k depending on year, seller, condition, etc. So you're still going to be looking at a $5k to almost $6k savings by going the franken route.
On cases, J&W used to have a phenomenal case. I'm not sure he still has it. The last couple examples I've seen were a different model. The NDT case is not worth considering. The best bet right now is try to to push Phong to see if he still has the good case, and cross your fingers that he does. But I think he has started hand modding some of his cases to make them look more like the older one. Probably not want you want to pay the Phong price for...