So since I opened my big mouth to promptly insert foot, I decided to stop posting peanut gallery comments and google searches, and make a few phone calls myself.
Called Plastic Bottle Corporation, who claimed on their site 5000 pc minimum (pretty low minimum for custom manufacturing):
Plastic Bottle Corporation; plastic bottle, plastic bottle manufacturer, plastic bottles, plastic jugs, plastic jars, plastic bottle manufacturers
They said that minimum only applied to higher end plastic bottles, for a 6 ml square custom bottle, the minimum run would be 25,000 units. To try McKernan, maybe they can help because they are a distributor and deal with a lot of different manufacturers.
I called McKernan:
McKernan Wholesale Bottles | Surplus Bottles | Wholesale Jars
Spoke with their senior salesperson at length, who had worked for McKernan for 10 years, and in that time, never saw anyone request a tiny square bottle. She checked their entire inventory for me, including overstocks, not even close (they have a HUGE variety of inventory, including some pretty weird bottle shapes). She said that they deal with Chinese plastics manufacturers for lowest pricing on custom orders, and the minimum order would be 100,000 bottles to go that route. She's emailing me a list of manufacturers that may help.
Meanwhile, I called Dynalab Corporation:
Contact Dynalab Corp.
Dynalab specializes in lab equipment, for both single and reusable, and they make LDPE and HDPE bottles. Talked to the sales person... they don't make bottles that small

. Sent me to Nalge manufacturing.
Nalge Nuc:
Nalgene | The original water bottle. Made in the USA. BPA Free.
- paydirt maybe.
Nalgene was purchased by Thermal Scientific recently. I spoke to one of Thermal Scientific's technical support group (the guys who design/test bottles). I explained what we were looking for, tried to get some info on new molds if the current molds do not exist. He said that to create a new mold from scratch, we're looking at up to a million dollars in pre-production. I said we're not trying to design a new car here, this is a teeny plastic bottle, so lets walk back a bit... can an adaptation be made with existing round molds? He said he had to check with engineering to see if there was a structural reason for why there are no square teeny LDPE bottles on the market right now already, smaller than 30 ml.
I explained to him that I am not part of the company making the inquiry, my company however has dealt with plastic bottling before (have an account with Mckernan already, which is why they were forthcoming with info). I also explained that the bottle must be able to hold e-liquid safely over years, food grade, ldpe soft, and containing no chems that can leach out into the fluid over time. That the reason their engineering team would waste their time on this issue is that while it's a very small company, it's one of the most well regarded and popular in ecigarette types, and are able to sell out all the inventory they can produce. Ecigs are already becoming a multi-billion dollar industry, so if this company can increase production, where will they be 5 years from now? Maybe it's worth their time? He agreed.
The engineering team want an email listing your spec requirements, Rob. I can't give that, so as soon as I hear from him, I will forward you his email and you can deal with him directly.
While I was typing this, got the email from McKernan rep... the list is all distributors... and unlikely to have this bottle in stock, to spec... I'll forward it however if you want to see it anyway.
Which email should I be forwarding to? The one on the website OK?