It's really a shame that that is the case. Doesn't sound right for a well established shop to not have their stuff together and run that long in excess of quoted lead times. Sadowsky, Ken Smith, Fodera, all take different amounts of time to produce, but the lead times quoted are not that far off from reality. They should work on that before it begins to do damage to their reputation if it hasn't already.
The thing that you should remember is that Zon basses are 100% handmade (no CNC machines are used), they are a VERY small shop and a lot of the wait time depends on what you want and whether the vendors that they deal with have what they need to finish it.
For example, you might have very specific woods in mind. Maybe you want a really dark ebony top and a light weight spalted alder body. If those woods aren't available at the shop, they need to source them... that takes time. Once the wood is sourced, it might not be dried, so that will need to happen... which takes more time.
That's just one specific example.
I can tell you right now that Todd's bass is the only one that they've made so far. So, if you want short scale headless 6-string with a set neck and then want to change it to 18mm spacing, it will be another first for them... that will take time to plan properly, if they can even do it at all at this point. Like I said, they don't have a machine that they can just reprogram... it's all built from scratch.
This isn't to say that a significant portion of the wait doesn't come from the shop itself... where you fall into the queue when you order and what kinds of fires start while you're in the queue can cause you to get bumped back.
There are many variables that add/subtract from the equation... so, when you call and talk to them, just understand that they can only give you the best guess they can give you based on that day, and realize that the bass you're ordering is a custom-made, one-of-a-kind handmade piece of art that will be flawless when you receive it.
That's all I can say, really... there might be a long wait, but man are the basses ever worth it.