Having trouble understanding your plans but ...
>> There are large lockers near the Shinkansen entrance at Shin Kobe
http://www.hotwire.co.jp/onegai/mission-2h.html
>> The Hilton is right across the road from JR Osaka station. It's a nice hotel and very convenient for trains to Kyoto and Kobe
>> You might also think about staying in Kobe.
The Crown Plaza directly next to Shin Kobe station might be convenient. Perhaps it would suit you to leave luggage there after you check out and then you can pick it up at the end of the day.