1 - Change the Trainz-Build.
2 - Change the filenames except for Config.txt. This allows TrainzObjectz to recognize files if you change anything on it (see #3), it will not recognize the word mapfile. Also need to add a line to the config for asset-filename using the new filename.
3 - Check the route in TO. If it used TRS2006 builtins, since some are not in TRS2004 they will show up missing. You either have to transfer those over, find them for download or replace them. Depending on how many you need, it could be some time before the route is ready. Or just run it without them but you may have to replace some stuff like groundtextures, track, etc. in Surveyor.