>The 2nd great-grandfather of my cousin is also the
>2nd great-grandfather of my deceased uncle. They
>both are the direct male descendants from this 2nd
>great-grandfather. (father-son-son-son, etc.)

>If I follow the logic of the Y-Chromsome passing
>from father to son through the generations would the
>result for my deceased uncle be the same as my
>cousin? I can't do the Y-Chromsome for this line as
>I'm the son of my uncle's sister.

It helps me to put this down on paper, with little lines and arrows... :-)

Since each of them trace male-to-male back to the same 2nd great-grandfather, yes your uncle and this cousin should have the same Y-chromosome.

Art, you can be the poster child for thinking creatively to find an individual to test!!