overnight trains in the off season should not be too bad. On two of my overnight trains i h\made a reservation, but one was to Pomplona for the run of the bulls and tons of people were trying to get to that. On the third overnight I made a few hours before i left. I think you would be ok but it does not hurt to make reservation
For hostels most of the ones i was in had lockers with the room coat or a small cost for a locker. If they have them there than use them. However small locks on your zippers is also good even just for walking around and your bag in on you back ( people can still get in and you would never know )
As far as missing important items
Don't leave any important items in you room.
When i went i put two two extra pockets on the inside of my pants one for cash and one for my passport, eurail pass, and flight home ticket. This worked great for me!!
Have a great tirp and keep us up-to-date on you travels. If you have any other questions just ask
T