First number one objective, make sure the donor frame comes with a VIN and the appropriate paperwork and the VIN is not associated with "salvage", "scrap", or is in any way "branded". In Ontario once a VIN has a "brand" on it (i.e. "salvage") it is a one way trip, no vehicle with that VIN can ever be put back on the road. So this is what is meant by "clear title". Finding a chassis in a salvage yard which is "clear title" may be possible ... or the salvage yard owner may immediately change the ownership into their name but branded as "scrap" or some such thing, in which case you are screwed.
You can fix this by buying a normal bike the normal way from a normal person selling a used bike. Just make sure the registration has a clear title (not "branded"). This is a perfect opportunity for someone to sell you, and for you to buy, a bike with a blown engine. A blown engine doesn't affect the registration status.
The forks and front end and wheels etc are not part of the vehicle's association with a VIN. The frame is. And NOTHING else. From the point of view of VIN, the ownership status of the vehicle makes no difference if you swap forks, swingarm, wheels, etc. But insurance will probably care ...
Likewise, the engine is not part of the VIN status. You are essentially going to have something with an engine swap. Again, the MoT won't care, but insurance will almost certainly care.
Because you are carrying on with an original vehicle's VIN, you don't need to jump through Transport Canada hoops - only a regular safety inspection ... which could potentially be more diligent than usual given the drastic nature of your powertrain swap and chassis modifications. Lights have to work, horn has to work, reflectors have to be there, tires have to be good, steering head bearings have to be OK, etc. One way around this - if you bought a running bike - is to get the safety and licensing done BEFORE you do the engine swap; this will of course mean paying for the license plate and keeping it valid during the you do your build ...
There is a way to change the "fuel type" on your existing vehicle ownership to a different type (Gas - diesel - electric etc). This should not be a big problem with the direction you are going ("zero emissions"). It would be a problem going the other direction.
Your biggest obstacle by going this route is going to be getting (legitimate) insurance. Mark my words. Insurance companies don't like motorcycles with after-the-fact engine/powertrain swaps and/or (what they consider) heavy chassis modifications and/or (what they consider) significant power-adders.
Other "kit" vehicles etc that don't use an already-registered "donor vehicle" can be extremely problematic to register. I know someone who bought a Titan custom chopper "kit" from the USA, had it completely customized and painted, and was never able to register it in Canada. He had to ship it back to the States and sell it there. Transport Canada insisted on obtaining documentation of compliance to the last letter of every conceivable regulation that could possibly be applied and much of it was simply not available. American-sourced "kit" cars, Factory Five hot-rods and Cobra replicas etc are almost nonexistent on our roads because of how hard it is to jump through all of the obstacles that Transport Canada sets out.
