I've gotten my Hog Bipe just about ready to cover, but I have one problem that may be a pain.

With the wings assembled on the plane, I have a gap between the top of the interplane struts and the top wing. If I lean the top wing so that the interplane strut touches the top wing on one side, the other falls short by 3/8".

I can't figure out what caused this to not line up correctly. The dihedral on the bottom wing measures right on with the plans. The bottom wing is seated flush in the fuse. The cabane struts line up perfectly with the holes in the fuse. The top wing sets perfectly level on the Cabane struts. But somewhere the tolerance stacks have me just out of whack.

Has anybody else had this issue, and if so, what did you do?

Sounds like the cabane struts are too long. The pictures of Hog
Bipes I've seen, the cabanes have a curve to them. Are yours
straight up and down? Is the top wing supposed to have some
anhedral to it? I haven't seen a Hog in person, but just going off
of pictures of them.

I have built and flown the plane and did not have that problem. It sounds to me like your metal cabane struts are not seated far enough into the fuselage.