Depends on the design.
I would create a PCB, using parts available at Digikey and/or Mouser, maybe other places depending on what's needed. Simple design is a couple of hours to come up with the design and an excel spreadsheet of part numbers. If new symbols are needed for parts that adds some time. Design will typically include ICSP header for re-programming, or somehow make those 6 pins accessible.
I use iteadstudio for small lots of boards. For 5,000 might be worthwhile to find a US manufacturer. Google US PCB manufacturer, you will find several, maybe even one close to where you are located, or in CA so shipping to cbas is cheaper.
Send drawings to Steve Brand at www.cbas-usa.com, he will quote you price for stencil creation, pick & place programming, and unit assembly cost. You provide a FedEx account number for return shipping. Simple board he might just assemble by hand for small qty.
For production, you go thru the same process - e-mail Digikey to get a programming quote - I've never had them do that.
Automated test box - will need to know what the card does, what the outputs do, etc.
That will drive the level of complexity and the hours to design, build, program if needed.
PM me if you want to pursue further. My wife & I are engineers from RPI, we've been doing this stuff as a small home business since ~Jan 2011, after doing it for industry for 25 years for much larger designs; imagine two 16-layer 8x8 cards mounted on a copper cooling plate, with ~80 SMD chips mounted each side, with high density connector over the top to connect the two sides and a 5x100 connector on the bottom to connect the two sides to a 32 layer backplane holding 26 other cards built the same way, all talking to each other over a 64-bit data bus. Little double sided arduino based cards are just fun little excursions by comparison.