So, after much testing, and even using a batch script to restart the service on both machines, I've identified the source of most of my input delay. Any time I have Rainmeter running, I experience massive input delay. As soon as I kill it, I have no noticeable input delay. I can even game on the secondary machine and rack up killstreaks without it running.
This sucks pretty hard, considering Rainmeter is used by a vast number of people for monitoring their PC, weather, to dos, and it's generally one of the foremost desktop customization applications out there. In fact Rainmeter is almost synonymous with Windowblinds for a lot of people.
I've gone through and disabled every program except for core Windows functionality, and Rainmeter, and I still get input delay on m y secondary machine.
I know it's probably not a quick fix. But please look into this.