And to accent the above reply: DO NOT BUY CHEAP BEARINGS

Honda makes incredibly high-quality bearings. It's not worth it to cheap out. Get the factory stuff and the engine will run just like a factory unit.

The Helm (factory Honda) service manual states that VERTICAL scratches along the cylinder walls are ok provided they are not deep enough to catch your fingernail. So, when you take the engine apart, check the scratches. If they're small enough, the cylinders can be honed. If you're worried about honing it yourself, any machine shop will hone an engine block for real cheap, assuming it's fully dissassembled and ready to be mounted on the machine.

There's also a good chance you won't have to replace the crankshaft main bearings. Since Honda engines use 5 mains for only 4 cylinders, the load is very well-distributed, and wear on the mains is very slight, if any at all. When I took my engine apart after overheating it (blew the head gasket, filled the crankcase with water...not good) with 170,000 miles on it, the main bearings were still very smooth, shiny metal. The rod bearings, however, were visibly worn. Some of them were worn all the way to the copper. So, be ready to replace the rod pieces. Mains *should* be replaced since you're doing an overhaul, but if you're on a budget and the mains look good, you can get away with reusing them.