Sit down, have a drink, and take a deep breath. Chances are things were already getting ugly by the time you found out so don't blame yourself. The mainshaft can be replaced but it probably wouldn't be worth the cost. I'm a cheapskate so here's how I'd go about it.
1. knock the remaining bearing pieces off the shaft and try to polish it with some emery cloth or 220 sand paper. You ain't gonna make it smooth so just knock the high spots down.
2. pull the outer race out of the transmission housing
3. cancel the order for the rebuild kit
4. check the bearings I posted earlier, if they don't feel loose don't worry about them anymore.
5. order a new input bearing and input seal (#9, #14) http://www.hondaautomotiveparts.com/...CLUTCH+HOUSING

At this point it's probably not worth dumping a bunch of money into, but I think there is still a chance to salvage it. That part of the shaft is just where the bearing sets. As long as there isn't any(or at least much) slop between it and the bearing, and it still provides a good interface with the seal it should work. The main area I'm concerned about is the where the shaft and the seal meet (circled) it needs to be pretty smooth and large enough to seal. When you get the new bearing and seal drop the bearing on the shaft and check for slop. Push the seal on the end and look for gaps.