I've had loads like that, it won't do any harm. What do you mean by the washer in the lower fork leg?
I'm going to guess you mean the ring above the top bush but underneath the oil seal.
It can go in either way but I bet you ask because is "dished"
The clunk and stiction is the bush moving up and down.
You can either hammer the ring flat, press it flat or buy new but it'll still do it to a certain degree.
I have had two nos complete sets of forks and they did it.
It's just manufacturing intolerances On new stuff.
Sometimes you can feel and hear it as a big clunk and sometimes you can't hear it but can feel it.
Don't worry about it, it's not abnormal, flatten the rings,
That's just how they are, they will still work, they won't break and will be safe.