One would hope that good security architecture would eliminate some of the conflicts you are now experiencing and make a more globally compatible system with revised and streamlined layers of protection. As noted above, such an implementation would probably take more than 3 to 6 months; but getting the agency heads on top of assessing the needs is a necessary first step that the EO calls for.
That's an oxymoron where I work. The only things these guys know how to do is keeping additional security programs on top of each other to the point where nothing works. As is it now, and I'm not exaggerating, half of the programming on our IT systems now are security related.
Heck, we have a joke, that McAfee is so bad it doesn't like itself.