I can't help with the primer alarm, but I'm not following how "Even without the primer alarm, the primer tube shroud rubs against the powder hopper on the way up." ? My powder hopper is well above the end of the primer tube shroud.
Removing your alarm adaptation the only real difference I see in your set up and mine is that my powder drop is positioned differently from a rotational standpoint. I had to install it with the shroud and primer tube removed to accomplish that, but it works better for the way my press is positioned.
I expand and drop at the same time (Using the PXT) and my die positions are the same as yours.
Sounds like you got it worked out anyway...
NRA Endowment Life Member.
The true danger is when liberty is nibbled away, for expedients, and by parts. - Edmund Burke 1777