I will answer these the best that I can.
The gray line is likely the 5V reference, that is the power for your sensors like TPS, Hall effect(cam and crank usually) sometime MAP, any additional sensors you add like fuel pressure or oil pressure usually need a 5V reference.
All of the sensor grounds need to return to the MS unit, there is a dedicated sensor ground wire you can run off of.
Your two wire sensors like air temp and coolant will have a ground to the MS and the actual sensor ground since they do not require power.
It does not matter what wires go on the injectors, and you will want to wire them to something like your fuel pump relay so they will only be able to operate when the MS senses that the engine is turning over.
MSEXTRA.COM has tons and tons and tons of info, look for the manual for your particular unit it will be there.
Here is the manual if you bought a pre assembled unit.
http://www.msextra.com/doc/pdf/html/MS2V30_Hardware-3.4.pdf/MS2V30_Hardware-3.4.htmlI have an MS3X running on my Barracuda ignition only right now, I will be doing the fuel side after the first of the year. I got all of my stuff from DIY they have great service so don't be afraid to e-mail them or call them with questions.