If you go into the MTO office, you can get a form to do a "sworn affidavit" which lets you establish the history of a bike built from old parts or from a bike which has been off the road or "in the barn" for a long time, without clear ownership history...
I am in the process of restoring an old 1983 Nighthawk, last registered in 1992, whereby the original owner is now deceased and the bike was on its way to becoming parts for a go-cart ... I will be writing what I know about its history and how I came to own it ... then swear to it at the ministry office. All on the record. All legal.