Second Half:

First of January
We begin the new year changing travel routes (or do you mean methods?). For three days we will board a pinasse, a slender boat of about 20 meters with a cover in the central part. It goes downstrean with a sail and upstream by engine. All the Niger is navigable and the trade along it is an important part of the economy of Niger. In this these three days we sail for 300 km to/until (see note) Mopti. The journey is slow and some of us get bored, but I appreciate this slow pace. Watching at the banks of the river there is a flow of images like in a movie: people washing clothes, people washing themslves, children that do not want to be washed, someone grinds grains, another build a clay hut, and so on. We cross (see note) other boats going upstream (completely) packed with people and goods. Sometimes in the daytime we have a short stop in a poor village, approachable only by river, where people flock around us to ask for whatever.

notes:

A little advanced style here: pinasse seems maybe a French word. If a foreign word is not in a standard English dictionary (such as: http://www.oxforddictionaries.com/spellcheck/english/?q=pinasse) then we will put the word in italics, because it is a foreign word as far as English is concerned. But common "foreign words" such as 'gratis','raison d'être', etc do not have to go in italics (as they can be found in a standard English dictionary).

to or until? to here suggests a planned destination or stop, whereas until suggests a duration (How far did you sail? Until Mopti, but we wanted to get to Xyz.)

cross - is the writer's boat also going upstream? Then I would probably write we overtake or pass other boats. We can also say come across other boats, no matter whether they are going in the same direction as the writer's boat.

style: if something is packed, it is packed; the word "completely" does add anything here. Although it is true that we will say "completely packed" in spoken English, in written English it is my opinion that the prose is better without using superfluous words. But the choice is yours, and "completely packed" is not wrong.

Correction of first half

Journey to Mail /3

The trek starts in the village of Dorou, it heads NE northeast and (it) ends in Yenodouma, where again we again get in the van to reach Tombouctou. Just to have (better: get) a general idea of the time you need: from Yendouma to Tombouctou it took takes us 12 hours and it's only 250km!

31th of December
The sightseeing in Tombouctou disappoints me, as/and there is not so much to see. Most of the buildings is are dilapidated, only in a few you can go inside only a few, and also these are nothing special. It was (is) more interesting to see (another and better verb?) the tea house, where the Tuareg do not merely drink a beverage, but they also perform a ceremony. 

notes

'NE' justs seems way to informal to me, so I wrote it out (in BrE, it might be written as 'north-east'.)

I think in English, "Timbuktu" is the preferred spelling.

'See' is good here, in my opinion, because it can mean 'to visit' (See definition 4.1 at http://www.oxforddictionaries.com/definition/english/see)

Again, you can stay in the present tense, thus 'takes' and 'is'. You do not have to stay in the present, but it makes the writing more vivid.