Train Shanghai to HK intead?

I was thinking of using the 144-hour thing for a visit to Nanjing and Shanghai. In the planning stages now, but one of the flights was to be to or from HK...probably HK-Shanghai, or reverse.
But train stations are allowed...so could I swap this flight in my plan for an international train to HK? I guess one to Shenzhen wouldn't work, it would have to be one to HK?
And the boarder crossing down there would be the 'time' they count for the 144 hours, or the arrival/departure time in Shanghai?