G'day mate, originals are hard to find. Totally TTRs had one last time I was on there. The tool kit inside is rather generic and similar if not same, can be found on Ebay (not labelled as Yamaha) I'm from Melbourne and had an 1998 Open Enduro for many years when they were first released, Had a ball on it. Can you post a pic of your new beast.
We used to have a bike breaker near us (now sadly closed) and they used to tip all the tools out from a "broken" bike onto a big table and there was always loads of Yamaha tools including the toolbox so other Yams must have used the same as the TTR.
It was easy enough to go through the pile to get the correct tools to replicate the contents of the TTR toolbox.
Worth checking you nearest bike breaker to see what they do with the tools