Following the "official" route makes planning relatively simple as there really aren't that many alternatives without adding considerable mileage.
The original challenge was to link the border towns of Hendaye and Cerbere by the shortest route, closest to the spanish border, staying always in france.
The 18 passes and 8 checkpoints tie you down to a straightforward route.
The main choices are whether to add the (optional) Marie Blanque at the western end, and whether at Ax les Thermes in the east, to take the original but now traffic-laden Puymorens or the quieter Port de Pailheres.
I did my Raid with the (considerable) help of Marmot Tours - you can see the route they follow - very close to the original - at this link
http://www.marmot-tours.co.uk/Road-Cycling-Holidays/raid-pyrenean.html
(as this is an Audax permanent rather than a tour you may get more feedback in that section)