Problem is most likely the shift drum and maybe the shift fork. The attached picture is from my old 954 that had missed shifts into second gear. Notice the damage on the drum. If the 99 is the same as the 2000-2003 929/954 the drum and forks can be replaced without removing the engine. The "How to" section seems to have disappeared from Fireblades site so here is a link to my write up on another forum.
How To ... - CBR 954 Shift Drum and Shift Fork Replacement - Parts required: Shift Drum Shift Forks (right, center, left) Shift Fork Shaft Shift spindle return spring Exhaust gaskets Oil and filter Clutch Lock Nut Ultra Black silicone to make oil pan and clutch cover gasket Tools needed: 5mm...
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