I didn't know that the SBox was effective for JAP PS2 - it looks like it isn't and I'm not at all sure you are going to get it to work. In any case you'd need a JAP Gameshark 2 and then probably 1.7 or later. It may be coincidental that PS backups boot OK because they don't depend on GS2.

In case things have changed with SBOX, have you got the single wire correctly soldered in place? That's a must if it is to work at all.

Modchip.com do a good internal modchip (8 wires) for the early Jap PS2s.