I never followed up, after some more digging and writing to the Ontario Archives, I received all the records from Alexander from the Hamilton Psychiatric Hospital where he sadly passed away. I was hoping it would answer some questions on why he left Scotland, and solve the mystery behind it all. It did include a photo of him which was pretty neat.
It doesn't say why he left for Canada, it didn't seem like he had a relationship with his boys as they aren't mentioned in the report. It seems he had been struggling with alcoholism for a long time, maybe his wife had asked him to leave.
It seems digging up the past can bring up lots of things, good and bad. Thanks everybody for all your help with this, appreciate it.