So, resurrecting this thread because I came across a thread on lag on XDA where the root issue was slow write speeds to storage. I've been seeing lag in my touchscreen response almost since I got my N7, and I'd figured it was tied to storage speed and also push notifications: it got noticeably worse when there was a push service running. Sometimes killing the service fixed the issue, sometimes not. Anyway, saw the thread on XDA with someone trying Androbench to see the read/write speeds. Normal N7 write speed is about 10MB/s, he was seeing 0.39MB/s. I was getting ~2MB/s. I figured hardware defect, but also that I should factory reset to check before calling Google.
Did the factory reset. My read speeds are normal now - between 10MB/s and 11MB/s. And the responsiveness is vastly improved. So if you're seeing lag, you might want to check your write speeds and if they're low, reset. Which sucks - it's a huge hassle to reset. But it's better than your tablet being periodically unusable.
Hopefully whatever causes this can be fixed in an update, or at the very least it recurs rarely.