Having travelled the route this year (by car) I'd make a couple of points.

Police checkpoints are a fact of life all over N Africa (and most of Africa in fact) and can be an irritation but not necessarily a problem. In fact I've sometimes found them very helpful. We were very happy to camp by one South of Gao after being threatened at a remote location. And on previous trips I've found them to be top-class at arranging lifts when hitchhiking.

The key item to have at any checkpoint is a clear copy of your "fiche" with all of the details they need to record in their ledger. (Name/Nat/DOB/Passport & Visa details/.... make of bike)

The (many) checkpoints in Algeria were very professional and there was never any question of baksheesh. They are located at the entrance/exit of every town and at every major road intersection. I would say it has nothing to do with raising cash from travellers and is all about maintaining security and controlling smuggling.

Before we arrived in Algeria, I was dubious about the guide requirement. Whatever the reasons, I was very happy to have one. Apart from being great company, he always led to the best places to camp.

As having a car tailing you through the country would obviously be very expensive, you could consider throwing the bike in the back and enjoying the ride in a beautiful country.

Finally, while we had no problems in Northern Niger, things have changed for the worse since April - you'll find details on this forum.