Ref: Is it possible to cross between Mali and Algeria?
The answer is yes, I did so back in late 2001. (Gao - Tamanrasset). Their is an Algerian consulate in Gao who can issue you with a two week transit visa for Algeria. The owners of Sahara Passion in Gao should also be able to assist you in this. I would also strongly recommend that you take a local guide who is familiar with the crossing and that you accept that there is a remote possibility of your meeting bandits. Sahara Passion sourced a guide for us who had a wife in each town!
We did not light any fires at night and camped off the road. There is a history of banditry in the region and it was quite a stressful crossing. Duration 3 to 5 days.
One other point, I doubt you'll make Timboctou to Gao in a 2wd. Its very sandy and rutted.
In a 2wd I'd probably cross to the south of the Niger at Timboctou (ferry) and head for Douentza and then take the road to Gao.
Good luck.
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