It is generally safe to "freshen up" a block using the same color bearings that came out- assuming no massive or irregular wear. As recommended, though, I would still mic and plastigauge everything to be safe. It's pretty painless with the engine already apart.
Don't know what the H and other designators mean on the rods, sorry. I don't think they have any value, at least, not outside of Honda.

They probably pertain to who did the assembly on the line.
The bearing matrix should be the same from year to year. Note, though, that the crank journal size changed starting in 98, so 98+ and 97 and earlier are NOT compatible.