Verifying userland has been updated is complicated, this is where having an established written record of updates is a good idea.
On Unix systems, when a file is modified the mtime value of it's inode is updated, using this information you can attempt to determine when it was replaced.. and compare it with the time the kernel was replaced.
When adopting a previously maintained system, regardless of OS, it's always complicated to reverse engineer the extent of the modifications made to it by the previous maintainer(s).
It is safe to rebuild both the kernel and userland again, obtain the vanilla source from an official mirror, and update it via CVS or using errata patches.
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