Wow, that is messy.
Having a weber clears up some stuff. I'm surprised you have an externally regulated alternator, I thought by 79 they were internally regulated. On your coil question, I would just watch the classifieds for a good used ignitor/coil from somebody. You have a good distributor, those are electronic, the whole ignition system in stock form is excellent and dead reliable. I have a 60 series with 250,000 miles and it has never faltered, I wouldn't mess with it.
Your charcoal system, or EVAP system as Toyota would call it is pretty intact. One line goes to the vapor separator, which is a plastic deal behind the metal cover behind the seat that covers the fuel tank filler. As long as that is all intact and hooked up, leave it. Toyota designed it so that the fuel tank can vent in any orientation. The separator drops out gas and lets the vapors come forward to the charcoal canister. There is another line out the bottom of the canister, that is the actual breather. The next line leaving the canister travels up and over the top of the firewall. This would have gone to an electric vacuum switching valve on the fender. That valve would have been controlled by the emmisions computer, typically bolted to the firewall behind the clutch pedal inside. I don't know if that is present on your truck, any of it, can't tell, looks like the plug is empty below the brake master. Vapor from the can is burned in the engine. The computer controlled when this would happen based on engine temp and sometimes speed of the vehicle. The idea was to only introduce the extra vapor when the engine was warm and cruising so that the idle mixture and such would not be affected. The other thing on the charcoal canister would have hooked up to the third nipple of the canister if it is present. This item looks to be blocked off with a bolt. This vacuum valve and its line ran to the float bowl of the original carb. Its purpose was to capture vapors from the float bowl and direct them to the canister while the vehicle was off, helped with boiling of the float bowl and smell of gas. When running that valve is closed electrically as vapors are burned in the engine at that time. Your Weber does not hae provisions for this. (I would be interested in the valve and lines actually.)
An easy fix, is leave most of it. You can remove the float vent stuff and cap it. The vapors can be burned with a simple valve, (DEMCV10039) that GM used for the same purpose. The two large ports go from the can to the PCV vent line, the small port can be teed into the vacuum advance line for the distributor. That should be ported vacuum and will only let vapors be pulled from the can whenever the throttle is opened beyond idle. I'm running this settup and it has been working great.
Other items. That distributor has two vacuum advance pods. One is the primary advance and will do 10 degrees I believe. The other is the High Altitude Compensation Valve advancer. It seems your HAC valve is gone. Not needed. Just make sure the advance vacuum line from the base of the carb is going to the inside advance port. Cap the other and set static timing at 7 degrees if you are near sea level, or add up to 4 degrees as the HAC did if you are over 4000 feet elevation. Lots of guys just run 9-11 degrees advance anyways. I've played with a range, really depends on elevation and engine. The line you have circled was the original vacuum advance line for primary advance, the plastic deal is like a speed bump for vacuum and slows down pulse from the carb, so the advance moves more slowly and smoothly, doesn't let timing bounce. You can try it inline there, see what it does, not necessary though.
The other line sticking out over the distributor is a vent for the cap. Hooks to the nipple near the coil wire on the cap. Not sure if you have the other nipple that was supposed to draw air from in the cab, through the cap and into the air cleaner. It keeps the cap dry and corrosive gases from eating up the cap contacts. Right now you are letting water right in the distributor. I would at least hook up the vent hose.
They make nicer allen headed plugs for the air rail holes in the head, but yours look capped fine. Probably rusted in anyways.
Fuel return is handled with your fuel pump. There should be a filter for the fuel line near the battery tray bracket on the feed line to pump. The return just dumps back to the tank. I would removed the plastic fire trap filter near the carb. Get some 5/16 fuel line and cheap bender from the bargain box at the parts store and bend up a new hard fuel line from the pump to carb and minimize as much soft line above the manifolds as you can. Just cut off the ends so you have bare line to work with and sip the hose over with good clamps. May even be able to find fittings that will let the flare nut work on the carb end.
Why on earth is you factory power steering not hooked up, it is great, use it. Also, you mentioned re-wiring everything. That is a huge job. Unless things are really bad, just fix what you can. Don't mess with stripping out the emissions wiring, it is a waste of time, just neatly tape the un-used plugs onto the loom and call it good.
Idler can be purchased for the air pump, also if the bushings seem good in the pump, you can easily remove the back, and remove the carbon vanes from the pump itself and then it will be useless and be an idler for now, won't hurt anything.
Hope that helps you clean things up.
