Re: 94 cbr 900 rr
could be a lot of things but I had something like what you're describing happen with my '92. turned out it was a dodgy wire causing a noisy and intermittent signal to cyls 1 and 3.. this became evident (to the tech, not me) when he looked at the signal on an oscilloscope which cleaned up instantly the moment he grasped the loom. replacing that cable entirely fixed the problem.
what brought it on in the first place was a jolt from a clumsy wheely, my theory is that the cable was already on it's last legs and the jolt snapped the remaining good strands in the core. after that the bike would start from cold but cyls 1/3 would not always be firing, after coming up to temperature with more prolonged usage engine would simply cutout entirely and only start again after being given time to cool down.