More info on the GTK series turbos here:
Turbonetics Owners Club

GTK-1000 Specs:
Compressor: 76mm Wheel, .70 A/R
Turbine: F1 S Trim 68mm Wheel, T4, .96 A/R

GT42R(s) Specs:
Compressor: 94mm Wheel, .80 A/R,
Turbine: 56 trim 94mm Wheel, T4, 1.01 A/R

As you can see, the GT42R is a larger turbo altogether. The GT series turbos are dual ball bearing, and the turbonetics GTK series turbos are single ball bearing. The GTK series turbos comes with an ultra lightweight F1 turbine wheel, and ported compressor housing. I would think that the GT42R would be capable of flowing for a little bit more power, but the GTK turbo would spool faster based on the above specs. I have not seen a side-by-side comparison though.

I'm currently running a GTK-854/650 hybrid turbo with water cooled jacket (a bit smaller turbo). You can get a turbo custom built if you contact a Turbonetics dealer and specify whatever specific features you need.