I will have a better look at the programming documents tonight as the atmega 88 has a built in bootloader area the Atmega 48 dosen't. The Atmega 48 is quite different in the programming methods available.
I am just hopping yamha didn't set any of the lock bits to stop reading or programming by spi. I am not sure why the rx and tx pads are present unless it is from development or with some luck it will allow the chip to be programmed. I would have thought it would have all of the program programmed by SPI, it may be that it loaded by the manufacture with part of a program by Spi and the rx and tx is used by yamaha to upload the T135 specific parts of the program later. The SPI are also available if you look at the left corner of the chip you will see 3 pads with traces going to the corner of the chip.
I may have a go at making my own cable if i am not to busy. Reading is stage one, dissaemble will be stage 2 and then stage 3 will be trying to program a modded file in to the CDI. After that it will be up to people on how adventerous they want to become.