it seems an good idea to switch the 40mm and the seacat, just watch out for what that does with your director setup
another option is putting 2 seacats (and 2 M44 directors) on platforms as far outboard as they will go on your hulls width. that is about what the dutch van speijk class had, one at each side of the hangar.
IIRC, the seacat on the counties replaced the 40mm/L70 on a one for one basis, so it might be a bit of an question why the 40mm is on anyways?
re the funnels on the counties: I just looked it up, and the funnels on the counties are on the centerline. the exhausts split up lower deck and join up at the upper level. that is of course possible as well.... do you have the same powerplant as the counties? this might help in that case:
https://dl.dropboxusercontent.com/u/632 ... rplant.png
the county had 2 boilers 4 steam turbines (2 low pressure, 2 high pressure, one set for each shaft) and 4 gas turbines next to each other, so that gives an idea how the uptakes and machinery spaces are set up