Just getting ready to drive the peninsula for the 4th time (in our Ford Explorer). Almost exactly 2000 miles from our house here in Southern Oregon to just north of Cabo. There is (or was) a small Harley store front in a new mall not far from the marina in CSL. I do not know if they rent or not. My advice? Enjoy the beach and the bars, scope out the place and enjoy your wife's company. Cabo has become very busy and can be bewildering in a car let alone on a bike. See if your hotel can set you up with a car rental and be prepared to pay $$$. Insurance is mandatory by law and that is where they get you. Also the rental outfits are notorious for "finding" a cigarette butt or bubble gum in the seat. Try to get out of town and up the East Cape. There are miles of white sand beaches with not a soul but that is changing. Your hotel can also set you up with various snorkeling and other adventures. Believe it or not, it can be kind of nice to let someone else do the driving.
I have a friend and an other acquaintance who have driven the peninsula on adventure bikes. There was or is a tour outfit that rents Harleys and does a guided tour. The trans peninsular hi way has gone through a lot of improvements but I cannot imagine driving it in my Glide. There are stretches (mile after mile) of wash board gravel where you actually drive in the ditch with pure dust. There is a place where you actually have to cross a flowing river where I have seen cars turn around. We have waited to see how deep the water came up on a truck before we tried it. It all depends on the season and tropical storm activity.
The police are often after the "little bite". That is what happens when you are not paid a living wage and see those rich gringos. On the other hand, We have found the average Mexican warm, gracious and always ready to help if asked.
Enjoy being in the tropics (drive up the hi way 1 to the nice marker that shows where the Tropic of Cancer crosses the road.) Cheers and PM me if you have any questions. We will be down for 21/2 months October-December.