RoyJ wrote:

If you are trying to resist shear forces,

I expect the glue to resist the shear forces. The screws are only
(hopefully) to temporarily keep the thing from flying apart if the
glue fails. Then everything would be remade.

you want the screw as large as
possible in diameter and you want to avoid having the threaded
portion in contact with the plates in shear.

Yes, that sounds desirable, however unlikely.

The bolt strength is not going to be terribly important, the
aluminum has a unknown strength but certainly less than half that
of the bolt.

My first choice would be a socket head cap screw in black
phosphate finish but all of those are fully threaded until you get
to over an inch long.

Using a locking nut (Nylock) would be a good idea in this high
vibration application.

You didn't ask but I would be looking at using a fairly high
strength aluminum like 6061-T6

Yeah, it's general-purpose 6060 or 6061 from McMaster. Once I know
what's needed, I would consider going for better aluminum.