The train station is at the southern end of Nouadhibou, it´s easy to find. Once you get there you go into the office, and look for the guy who gives the prices, and then another guy who tells you if there is any place or not.

I took the train three times and each time there were bikers on board. Once I took the three bikes in my van (early 1999), the price then was UM4,000 (probably gone up but in the van they paid nothing. The other time they laid the bikes flat onto the platform and tied them down. After 12 hours on a bumpy track one of the bikes was badly damaged (mechanicaal) the other two were ok but looked pretty bad. The last time I went they had another system which involves tying the bike to the back of one of the cars on the platform, the bike and the car were badly scratched. I´ve since heard that they have another system which seems to work by standing the bikes up and strapping them down, but I don´t know if this works or not.
On the train from Kayes to Bamako they got four old tyres, tied them together and laid some Swiss guys bike on that (a new Varedo) it worked perfectly.
If you want to drive on the tracks it seems to be quite easy for a bike to drive along between the rails, we managed 25km on a 125 Vespa withput any major problems and I met a few bikers who did it without any problems.
I suggest you go to the train station in Nouadhibou and let them show you how they intend to transport the bikes so you can make your own mind up.