Dave,
He is not talking about changing his (expired) American license to Japanese. He has a Japanese one already, but it is only good for automatic transmission (AT), and he wants to convert it to one good for manual transmission (MT).
The international driver's permit can be renewed, but it is not valid in Japan after you have been here 12 months, so I recommend against spending the money. It won't be legal.
Oh, and if one DOES convert a foreign license to a Japanese one, it costs more than 3500 yen. Closer to about 10,000 if you factor in all the costs. You have to pay 3000 yen alone just to get it translated at JAF. (And, Americans cannot just convert; they have to take the written and driving tests, but the OP's situation is moot. He has the J license, and needs to keep renewing it because his expired American license won't let him just breeze into a drivers license station and take the tests again. He'd have to go through the very expensive drivers ed courses if not for his J license already in hand.)