I found few wires when taken out the lower portion of dash and cleaned carpet wonder what they are for?

First off this 3 wires that come out of from the same wire as audio jack what are they for?

 

Looks like you have a lot of plugs/wires pointed out....Most likely for options/accessories your truck didn't come with and factory speaker wires.

Download and study a wiring diagram here : http://www.toyotaminis.com/forum/threads/toyota-factory-service-manual-link.21369/

 

Actually, i couldn't find a good diagram in that link...

This one has a lot of dead links, but this is where i downloaded a fsm for the 1985 pickup/4runner (can use for reference on newer models):

http://www.yotatech.com/f128/toyota-factory-service-manuals-fsm-all-years-156128/

 

In the second picture, I know the blue one that plugs into the black square is for the clock. I just pulled one from a 4runner last week and it installed pretty easy. Two screws into the bezel and then it clips into that plug. The female plug in the photo next to it is for the A/C button.

The rest are speculation, and I could be way wrong, but here are my guesses:
I'm completely lost on the first picture, sorry I can't be of much help there.

Picture 3 looks to be the right spot for a glove box light switch, and picture 4 could be for the glove box light. My next guess would be A/C components, but not sure since the controls are mostly manual other than the on/off button.

The last picture, the pink and purple look like speaker wires. I think my speaker wires on the passenger side are that color. Not sure about the other one.

 

1- i have no clue, could be the light to the ash tray and parts of the radio

2- Clock and A/C button

3- glove box light or a component of A\C

4 - Another a/c plug

5- pink and purple are speaker and the other i cannot say.....