I don't know about Mexico, but I had to register a homebuilt boat in the US.
I had to go to the tax office to explain my situation.
They in turn, sent someone down to where I built the boat and I had to show receipts of materials, photo's, etc. It was quite the ordeal.
Then they issued me a registration Number, which I had to "permanently" inscribe onto the
hull near the stern, which once again, required a visit from the same person to inspect.
After this, I was able to get boat registration stickers.
Hope this helps.