Dear Sue,
I have already admired Barley on a different thread (yes, he's blue-roan and tan) and I am already quite confused since my 9yo golden bitch is called Barley !!
It would help if you could let us know something about his 'previous life' since I work for the Blue Cross and we are used to dealing with dogs who have had (at least) one home and trying to get to know what makes them tick ...
The really important time for puppies is between say 4 - 12 weeks when they are really impressionable - after that time, you have to work much harder to get them to react in the same comfortable way, simply because they may not have had the sensory input that a normally-homed puppy would have had ... They think the hoover is a monster; the dustmen are fiends (which they sometimes can resemble, but if you ask them, they will bring doggy treats, and you can let yours out so that the fiends can ingratiate themselves over the gate - works with Postmen/ladies too!).
Having a place of safety, like your crate, is nice, but perhaps you should restrict that to sleepy-time and night time, and make it more open and accessible during the day. Doooo 'baby' him and cuddle him lots and make him secure, but on the other hand, take him out and (whilst he feels cuddled and mummied) show him traffic, shoppers etc. and above all, other dogs and their owners ... don't be tooo protective, so that he feels as though a confrontation is about to happen, rather be jolly and 'cool' and if he yelps or jumps behind you, and the other dog is just socialising, bring him out again and reinforce that all this is OK !!
It would be really nice if when you are on a local walk you could find someone with a dog who is cool to Barley and lets him pounce and fiddle and generally do all the things that young dogs need to do to find out their own social hierarchy ... such people DO exist, and don't be afraid to let him off-lead to play ....