Past perfect or past simple in combination with present perfect?

Solution 1:

In most contexts the first of the three would be the one to use. The other two would be possible only in rather unusual circumstances.

You can use either the simple past (typical American English)

I examined the document you gave me and ...

or the present perfect and the simple

I have examined the document you gave me and ...

I've examined the document you gave me and ...

If you're writing to a colleague, there should be no reason not to use a contraction ("I've").