Purchased new clutch master cylinder but when it came in box there is no boot over the end of cylinder where the rod connects. Does not seem correct since looks like theres a groove machined for a boot to fit on it.
Right in front of Nissin on civics theres a boot but there's no dust boot on this S2000 one.
Anyone know what is going on here?

 

Did you bother looking at the old one? There is no boot.

 

Dont assume i had an old one.

 

There is no boot over the end. You can see the seal under the dash. It is common that they leak because the clutch fluid is seldom changed. You can see it leaking from the seal under the dash.

Here is a great video on it: