Hi Cullen,
Thank you for this workaround. I did as you said, and it works, unlike copy and paste from Numbers 2.3 to Numbers 3.0 🙂.
In Numbers '09 (version 2.3) I created two Custom formats.
Column A is the inbuilt Date and Time format showing only the Date (my region's date format is Day Month Year).
Column B is a Custom Format to show short Month, space, short year.
Column C is the inbuilt format for Number.
Column D is a custom Format to show leading zeroes.

Then I did as you said and saved the Numbers 2 document (as a document for future use, not as a Template, because I am not sure how Templates are shared between the two versions on Numbers).
Then File, option key > Save As... a new name to preserve my original from harm by Numbers 3.0 😉.
In Numbers 3, (as you said) open the spare copy and the Custom formats are indeed listed. Format Inspector > Cell > Data Format

And they do work. Here is where I edited the cell content by entering new values from the keyboard:

I shall place a link to this thread on the thread named "Workarounds in Numbers 3.0?"
https://discussions.apple.com/thread/5512949?answerId=23622372022#23622372022
Thanks for this.
Regards,
Ian.