Aha, finally someone who is doing exactly what I'm doing. Got it all lined up and ready to go so I'm going to save you a lot of time here:
1. You stamp the frame, you will get caught and will have to dispose the bike and probably face a hefty fine or jail time. Transport Canada has a direct link to Honda and Suzuki with valid frame numbers. You will also have to show registration documents. Just ask Windbell Motorcycles in Squamish.
2. Send the bike as parts and the same penalty applies. People have been doing this in the past and they will consider the same penalty if they see you are making a shipment of parts to make one bike. This is how Gary Goodfellow use to do it when he brought RGVs into Vancouver in the early 90's.
There are a few ways you can do it legit:
1. Do exactly what you are doing, MC21 frame with everything else as a MC28. The conversion is fairly easy according to one of the shops in HK that specializes in NSR. He had one done up for a racing bike. So, in this case you can send back the bike in parts and assemble it in Canada as long as all the components match the reg document.
2. Import only certain components of the bike and source the rest with North American Parts (ie. wheels, front suspension, pipes, etc...). In this case, all you need to prove is proof of purchase as you will be registering as a home built.
Hope that helps.
rip