I was curious if there was some thing that would cause me to have to relearn how to fly the 747-400 in the newer version, or if  all of the updates were things like systems and features rather than controls?

I don't know what you mean about controls.  QOTSII is a huge upgrade over the first 744.  Most of which is systems logic, display logic, modeling and FDE.  Lot of systems have also been added that were never there.  

Having said that, if you know how to fly the B744, or any modern Boeing, then your learning curve should be short.  In reference to how operations are performed to start and manage the plane during a flight, I don't know of any major difference. There may have been under the hood logic in the first queen that has been changed to closer match, but you have have to know the bird inside and out to see those changes. 

In terms of FDE, yes it does handle slightly different, mainly in landing to my recollection. It's easy to put her down, but I felt the first one was a little easier to land. All in all, the handling differences seem minor and landing is easy though. A few flights and you should have it down.