Not too long ago I disconnected my speedo cable, rode the bike for about 100 miles and then I re-connected it. Now the speedometer, odo, and trip don't work. I am certain that it is connected correctly at the clock, however I am able to pull the inner completely out, so that doesn't seem good. I'm not sure how it connects at the point of origin down by the clutch area, and this was probably stupid too, but I messed around with the phillips head screw at the area where the speedo cable meets and now I can't shift into neutral. What have I done!? Is this coincidence? The manual only allowed me to mess things up so far.......

It sounds like coincidence. My advice would be to stop fiddling until you understand. Depending what kind of person you are, take it apart and look at it until you figure it out, or find someone who is that way inclined to help you out. It's a basic mechanical cable, assuming neither bit at the end is broken.
The cable inner is meant to come all the way out. Take it out, wipe it with WD40 on a rag and check it's the full length of the cable, as it is possible it has snapped? At the bottom it's just an interference fit, like a screwdriver into a slotted screw. Take ti apart and have a look.
This will teach you to fiddle about
