Auto down function I'm certain exists on this and resetting it wasn't a pain either. We had to do it when our battery died in our Crosstour.
I also didn't read this well enough, as the OP stated that apparently NONE of the windows can be controlled from the driver side master switch.
96-00 Civic sideskirts can be made to fit on these 4th gen cars.
OEM sideskirts for the EF2 were available on Euro models, so they may be tough to source.
Just find another handle and lock from any other 6th gen Civic. You say you have a '96 Civic Si, are you from Canada?
A secure garage, or don't drive a Honda.
Because there is no "Ex" model in Canada and the Canadian market EM1 is badged as a SIR.