I didn't think it was possible to assemble a Japanese T38/99 bolt incorrectly! I can't do it.
Mmmmm, is the firing pin in the cocking notch or is it all the way forward? If it's decocked you just need to draw the sear engagagement protrusion on the rear of the firing pin rearward and engage it in the cocking notch. It's easiest to do if the bolt is removed from the rifle. (The firing pin tail should then be in line w/ the safety tab and 180 degrees opposite the bolt handle.) That will free up the safety for removal and/or normal function, unless there's something REALLY odd going on!