Left over from the T5 swap, I have a 4 prong connection, which I know whas for the TC, but then there is another 2 wire connection that I left hanging. What is that for?

My car was origiinally a 87 v6 700R4 and uses a speedo cable. It does not have a VSS. What should I do with this 2 prong connection? Leave it hang?

 

your left over wires are probably for reverse lights. Depending on the transmission, there is probably a 2 pin connector in the side of the tranny for this. it shouldnt matter which way you hook them up because it is usually a simple open/close circuit switch. just be sure to solder any wires under the vehicle exposed to the elements. it will save you from a huge headache later.
As for the left over VSS wires, you can cut them off, just be sure to cut one wire at a time and at different lengths so that they do not short to one another or you will be blowing fuses.