You should rephrase your question. I read it several times and I can't figure out what you are asking, unless you are asking how to manufacture your own Jamma boards?
Or are talking about reprogramming them yourself? Well all those 3 in 1, 4 in 1, 9 in 1, and 39 in 1 boards are the exact same board. I find it especially arrogant that they charge 3 times as much for the 39 in 1 board when it is actually cheaper for them to make (they are all the SAME THING, but the 39 in 1 has no user choice on the games so there is no labor involved in putting the exact games the customer wants on it).
Arcadeshop sells a similar programmable board, which you CAN program yourself with a serial cable. The list of games it supports isn't very impressive though.