This is a subject I know like the back of my hand at this point.
The plugs next to the fuse box are a large 8 pin Grey and a medium Brownish/Deep Red 8 pin connector (or 6 idk, its still pretty easy).
the two you are holding in your hand in the first picture are actually as followsLarger 8 pin connector is skyline Chassis power and smaller 6 pin grey connector is part of injector harness, and the other clip off to the side thats slightly broke is your VTC plug.
That one larger connector does not get used at all, the grey connector plugs into your injector harness. and the last one plugs into a solenoid that should be screwed into the side of the head.
If you trying to wire it yourself, which is what I believe your doing here... take a few minutes and look at these two articles.
http://www.rbforums.org/pics/rb25diagram.jpg
http://www.rbforums.org/pics/rb25s13.jpgthose will help you get started.
Post back with more updates.
Email me if you get really stuck, I went through EXACLTY what you are going through right now
stevespeed@gmail.com
The Wiring DVD gives you a descent prespective on which wires to cut and splice but it would have been really helpful for the camera to zoom in and actually show upclose which ones, but Yuri did a good job none the less for laying out how to do it.
The dash interface also is really simple and I highly HIGHLY recommend wiring up your connector for the service port, that comes in SUPER handy.