You'll do fine. Baja is always my choice for transiting South. Very Hot at present everywhere. Once you cross over to either Mazatlan or Topolobambo, you can get rain. But heavy rain starts South of Mazatlan. This is the heart of the rainy season, but you knew that, right?
The Cent. Highlands can have a bit less rain and hopefully will be a bit cooler. Get a good guide book (I'm sure you've got one).
In Baja you could do some off road exploring, depending on what you're riding. Further South on the Mainland will be more and a bit harder rain, more rain on the Coast. But the rainy season is also stunningly beautiful. The smells and sights are great in the Sub Tropical zone along the coasts South of Puerto Vallarta.
If you're lucky you will get dry mornings. Best time to ride. By Noon it can cloud up and could rain anytime into the night.
Give yourself time to become accustom to Mexican driving habits. Watch and learn before you jump in.
Cross at Tijuana and get your TVIP either there or in La Paz.
3 weeks is not much time. If your a beach person stay on the coast. If severe heat and rain bother you, get up into the Highlands and see the old Silver mining towns .... some of the most beautiful and historic in Mexico.
Its all good. Zacatecas, Guanajuato, Morellia, San Miquel De Allende, and more. Some great roads in those mountains but the mainland now has a LOT of traffic.
For beaches I prefer Baja's empty ones. The Southern Pacific coast of Baja is fabulous and deserted .... if you know where to go.
I hope you've got tire repair stuff and decent tools. Keep an eye on your fuel in Baja. Always top up when you can. If you hang out in Mulege' area
you may hook up with other riders. Lots pass through every day. La Paz too is a sort of Hubb for travelers coming and going. It's off season now ....
so you Cannucks have got it all to yourself!
Have fun, ride safe, don't fight the heat ... adapt to it.