Is it possible to use the 2006 remote in an 05 Baja... will it work?
The 06 is the 'upper' remote in the picture below. (These are not perfectly to scale, but the 06 is indeed slightly smaller and more intuitively designed than the earlier ones.)
I don't see why not. Open it up and see if it has a 8 digit number like the 06 remote. If so, it should work. Try programming the remote using the instructions in your manual.