Do I disconnect the rod from clutch first?
Nope, leave the hydraulics completely intact. You're testing to see if the auto-adjust valve in the master cylinder has been pinched off by overextending the rod. If it has, you won't be able to push the slave's rod back.
For the record, if it is pinched off, I unfortunately still don't expect that to be the main issue...just something you might as well fix while you're there.