[FirstOwner69]

Refer to post 16 for picture links. Responses in red...
Ugh...I already don't like Flickr.

OK, maybe this will work!

Below is a pick of the driver's side wiring. I think I have it right here except for the little guy at about 1 O'Clock. Does this connection bolt to the nut pressed into the core support? I have it pulled up into the nut with a copper wire. (I think it must go there as it seems like it wants to and has the impression of a nut on one side).
Yes, that is also the same location mine uses for the driver side marker light. It would help to know what year your truck is and if it has lighted side markers or reflectors. I have seen the side markers wired a couple different ways on trucks that appeared to be unmolested.


Next is the "Junction Block." I think I have this attached to the fender correctly.
Block is attached correctly. Need to verify what the 2 wires are and if you have gauges or idiot lights. If you have gauges there should be another wire there. Refer to post 6 for wires. The factory used a 12 gauge red wire that went across to the alternator and regulator. The black wire that goes forward toward the core support may have replaced that wire, but I have no idea what the cylindrical object in the wire is or if the wire is correctly run. You need to take a hard look at this to find out what's going on there. Might be time to summon VetteVet! Perhaps you should send him a PM asking that he take a look at this thread.


Next is the ground wire that goes to the core support behind battery tray (passenger side). Is there where this goes?
Yes, if it's from the headlight. It may also be where the right side marker light is grounded (if you have lighted markers)


Here comes the fun. The cable with the blue tape is the positive and runs to the starter motor. It also has a wire that attaches to the Junction Block.
That is correct IF the wire to the junction block is a fusible link. I'm not sure how to verify that. If I were you, I'd replace both battery cables.


The pic I tried to get of my negative cable and its attached grounding wire turned out very blurry so I didn't include it. Here is a shot of where both battery cables go. Negative is attached to the engine but where does the smaller wire go? (Smaller wire is attached to the negative cable at the battery terminal end. Mine has yellow overspray on it so I assume it was near the fender from factory and when truck was painted in 1990).

In this pic the "smaller wire" from the paragraph above is looped into the cable end just to get it out of the way. Where does the "smaller wire" attach?
I've never seen a truck with original cables that had a wire off the negative terminal. It probably wouldn't harm anything to have an additional ground if you choose. It could possibly go to the location behind the battery. As mentioned above, I'd replace the cables.