What is required in Ontario for Custom made Frames?

Normally with a restoration, there is no special inspection or certification needed. If asked, you "repaired" the old frame, not replaced it. If you replace one frame rail, and the cross members, that is a repair. If you then replace the other frame rail, it is again a repair. No one needs to know that you did both "repairs" at the same time

Build the new frame to match the old one

You definitely want to consult with the MTO on this, even though they can be a huge pain in the balls, but I don't believe you need any re-branding of the vehicle.

The branding program in Ontario was largely developed with damaged vehicles in mind, not situations like yours. You might have to register it as a custom, depending on how much work you're doing in total, but the branding applies more to vehicles that are a technical total loss.

You'll definitely need to have the frame checked out by an MTO-approved technician, but I think a usual safety certificate will do. But note those important words: I think. You'd probably want to verify it with the MTO themselves, because they're the people that do that stuff for a living and their word is law.

If you end up talking to an idiot who doesn't understand your question, and you might, ask for a supervisor. And don't mention nuffin about branding and structural inspections, or they'll start thinking this was an accident and you'll spend hours convincing them that you're just restoring it. Never let those people make assumptions, because they're stubborn as all hell even if you correct them several times.