As far as mixing different rated cable and jacks, it'll work but you do risk having the connection run at the highest common speed (100 megabit even though you're using cat6).
That should only happen if one of the pins fails to connect.
Gigabit isn't as sensitive as some make it out to be. I've been running gigabit networking over about 150 feet of 4-pair CAT3, with two splices in between. I shouldn't even be able to use 100mbps over this mess. Shockingly I've been using it this way for about a year. It hasn't skipped a beat, and I transfer big images over it all day.
I intend to run new CAT6 at some point for peace of mind, but it's just not an easy task where my main PC room is located and shear panels that block the path in the attic.