I got this XT from a buddy who wasn’t mechanical, never pulled it apart.
Clutch was sticky, water in everything, so I fixed all that and replaced the rusted clutch plates with new ones. When I got the new set, there’s a smaller clutch plate, but the original didn’t have this smaller plate... where’s this go?

I left it out, mimicking the original parts, but doesn’t seem to want to get into neutral. Gears can shift if I just kick em, but clutch doesn’t seem to help.

Ideas?

Can you identify it in the diagram?
Clutch diagram

If you can, it may be what the original problem was all along.

Hmm.
I’ve got a 2002 XT, which the diagram you sent me (2004) is prob the same.
The clutch friction plate I have in my possession is #18 here: https://www.yamahapartshouse.com/oemparts/a/yam/5004369df8700209bc78c22b/clutch
Maybe my issue is that I bought the wrong friction plates. I got them off bike bandit iirc. I’ll have to double check.
Looking at the diagram you sent over, all the plates are the same. I’ll hafe to pull my basket apart and verify that I have the correct number of plates.
Looks like 6 of the friction plates, and 5 clutch plates.

Yeah, your diagram is looking different.
Here's the '02
'02 clutch
Looks the same as the '04
Didn't know what year bike you had.