So I have my emissions removed, along with the solenoid rack. Can I just cut out the plugs and wrap over them or will it cause problems? I don't want to take the whole harness out and take them out from the pins, I plan on keeping the major wiring work for when I get a standalone, just don't want the plugs hanging around for now.

Also, on the rear iron there is a ground wire. However, it doesn't go anywhere. It is broken and came unraveled about 8 inches after the ground. However, there is a (newish-looking) ground wire with one end fastened to the firewall and it ends in a ring lying near the first broken ground wire. I am thinking it was put in somewhere along the way as a replacement. Am I right in my thinking or does it go elsewhere?

I can take pictures of what I am talking about in the morning when its light out.

 

Sure, you can cut the plugs off and tape up the ends of the wires.

And the ground your talking about is supposed to run from the top of the transmission bell housing to the firewall, near the wiper motor.

 

Yes you can cut them.

The cut ground you are referring to sounds like one of the resistor capacitors possible the one for the oil IIRC but it is a capacitor of some sort at the least. I have never found an FC to have ill effects with it broken who knows why but if you can fix it go for it. HAILERS or Wayne88FC will be able to give you exact correct info on this part so you might want to post some pictures and wait for them to reply if you are in dire stray to know.

The other wire is indeed a ground and clips onto the firewall the main ground is located under the vacume rats nest on the rear iron.

 

One ground goes to the Firewall
There is also a Capacitor on a wire that Goes to the clutch slave and it has something to do with the Oil Pressure sender.So if that is Off,do not just use a Ground wire as a replacement.