Where to start...

#1
Check the main engine fuse (should be the 80amp joint in the center of the engine fuse box) bet you its blown. Good news a new fuse is about 2 bux at autozone. While you're at it you might as well get replacements for all the fuses and keep them in the car. Cuz you'll feel like an ass if you have to pay a tow charge for a $1 fuse going out.

#2
In pic 4. That black plug w/ the green and red wire is for the Aux Fan temp sensor. As your sensor bung in the WP housing (see pic 1) is neither drilled, nor tapped for a sensor, don't worry about it. The fan is about the size of a CD and doesn't do much anyway.

#3
That Green backed plug in pic 2 is the Temp Thermo Sensor. It tells the ecu what temp the engine is running at so it can thus provide the proper amount of fuel. If this is disconnected your car will probably run like shit. Either really rich (hopefully) or really lean . If that broken green plug is supposed to plug into the thermo sensor (ie, there is nothing plugged into the thermo sensor currently) you should get a new plug and fix that with great expedience.

#4
Sorry, but I really can't help too much w/ the alt situation. Is the alt putting out voltage? what was it putting out? What signal does the alt need to charge? last time I checked the alt ran when the car ran, and it put out voltage to power the car and charge the battery (if above 14V). Not really clear on what the issue is here.