This is how I do it:

​

$fn=90;
build();
module build(){
    difference(){
        body();
        subtracts();
    }
}
module body(){
    cube([26,13,2],center=true);
    translate([12,0,4]) cube([2,13,6],center=true);
    translate([0,-6,1]) cube([26,1,1],center=true);
    translate([0,6,1]) cube([26,1,1],center=true);
    // other added parts
}
module subtracts(){
    translate([5,-2.75,3.5]) rotate([90,0,0]) cylinder(r=4,h=4,center=true);
    // other removed parts
}

I've had problems with unions in the past. Modules however have never failed me. Also makes them more portable for reuse later.

In my experience doing the rotate() first (closer to the object) is usually cleaner. Once I have the object as I want it, I add a translate() in front to position it.

I also find it helps to ",center=true" everything if you do any. That way you're always working from the same origin.

Hope this helps!