Ship your luggage to HND from the hotel and take the train. It's incredibly easy. The change at Shinagawa is very clearly marked and every announcement on the platform/train is made in English/Japanese. They repeat every 30 seconds or so. If you're truly lost, ask any of the many JR station attendants and they'll either answer you themselves or find a colleague who speaks English.

Don't forget to pick up some ekiben at Kyoto Station before getting on the train.