After a bit of a break, I'm back to it. I ordered the clutch centring tool from eBay. After shipping to Canada, it was a bit pricey, but I think worth it:
I cleaned up my transmission/input and clutch splines really well and used Staburags. I didn't catch a photo of the staburags that I put on, but I used very little and applied it very thoroughly. Here are a couple photos of the splines and the clutch pack being centred:
I torqued the clutch bolts to 18 Nm because I decided to reuse them. It took a little bit of adjusting, but I got the clutch pack centred and the tool was spinning freely.
The transmission is now back in, and I have to say that this makes it feel a whole lot closer to being ready to ride. I still have some other maintenance to do before it is completely ready.
Thanks everyone for all of your help and guidance. If it weren't for your suggestions, I would have probably not changed the clutch nut o-ring or used the correct tool to centre the clutch. I will keep you posted with some more photos as things go back together.