That little thing on top of the air box looks like mine ('93 3.0L). It seems to be a vacuum switch that actuated a damper in the intake line that pulled warm air from a shroud on the exhaust manifold. Temporarily just make sure it isn't causing a vacuum leak. If you live in a cold climate, you may want to eventually make it functional again. I'm in SC and decided to get rid of it when I modified my intake.
You're getting a bunch of good advice. Just take your time, do the research and keep knocking out these problems. It can be done.
Those red tap connectors in photo #11 should be removed. Inspect the wires for damage and repair as necessary. That style of connector is convenient, but can cause trouble. If the wrong size is used, it can cut strands inside the wire and reduce the wire's current capacity. If it were mine, I would remove the taps, cut the wire, then strip, twist, solder and heat-shrink it to restore reliability. I have been making similar repairs to my truck recently.
Also, tape up all loose wire ends until you can either reconnect them where they belong or remove them forever. You don't want a loose wire end shorting to ground and causing intermittent problems or damage.