Firstly, he could haven a medical problem re seeing......worth checking that out but he also sounds very anxious , he feels vulnerable so prefers to go toilet where he feels less vulnerable, so inside hie home........pups naturally do not soil their homes but he must have felt the need to and would be very upset by soiling his bed.
he needs his confidence building up, time consuming but worth it, you are right to take him back to baby stage, he should improve in his own time. I would not remove the crate but leave it open with newspaper around at night time, if he is in your boot room, it's not too bad, ours sleep in a boot room with open cages and although its rare, we sometimes find a poo in the morning, our youngest labs are 3,
our 3 year old Yellow Lab is also nervy, it's her traits, her mum is a bit and so is her dad, she is such a good dog she never gets shouted at or told off, yet she hates strangers coming up to stroke her etc, she likes to sniff them out in her own time, I suspect your boy is similar, do not force him , ignore him and he will become more confident, make sure he meets lots if people.
training in anything will be great, Li would bet he will be a highly intelligent boy,.....would love to meet him......Hope I have made sense as I a m writing this without my glasses......XX