Yes there are things to worry about, the crank bolt is not a fun thing to get off off hondas, they have a metal key in them that seem to be a b*tch to get out sometimes. IF you can try and get a crank holder from a autoparts store as it sometimes will be very hard to come out, even with a impact gun. If its a manual, you can take the clutch shield off and hold the fly wheel with a screwdriver and it makes it much easier to get off.
As for the marks, there is one on the cam and on on the crank pully, but depending on how old it is, they sometimes wear off, but i hardly happens. it goes the same for hondas as almost all cars make sure its TDC and line it up. If you need instructions from a helms i can probably scan it, just let me know.
As for the water pump job itself, its not that bad, but make sure your coworker is using oem parts, as aftermarket pumps can lead to disasters with that car. Many people on Honda tech have reported using aftermarket pumps and having them fail in less then two mounts, (Mainly due to the way they drive them, but i never said that).