Lost items in Photostream

I have had a problem with Photo stream since upgrading to a new iPhone 6+ and using ios 9.0.2. All of the upgrade I did through iTunes and restored from a backup from my old iPhone 4. (it was a nightmare but I succeeded in the end - at one point I thought the phone was completely broken). I can see I have 1,900 photos in Photo Stream but only about 1450 of them have appeared on the new phone. This was a few days ago but not further photos have appeared. Two years of photos are missing, same with notes and same with messages! I backed up my old iPhone 4 to iTunes and used that backup for restoring but I guess it doesn't back up notes or messages or of course the photos in iCloud. I have no idea where all they all are or more to the point how to get them back. Has anyone had a similar problem? Or any ideas how to get the missing items back? Many thanks