The vacuum valve next to the distributor is a thematic valve and is in the cooling system, it closes off or applies vacuum to components as engine temp goes up. My guess it was for the hot air/ cold air doors that were in the stock air cleaner assembly, ignore it not your problem.
The EGR valve could be stuck slightly open and causing the concern[internal vacuum leak] Take it off and either make a block off plate and add new gasket for it , or take it off and blow trough the side without the pintel in it, if you can blow trough it it's either stuck open or leaking past the shaft.
Me personally I would just make a block off plate for it and call it a day.
That truck running points or duraspark ignition? Cant tell from the pics.
Cap looks kind of dirty and the inside might be worse. A timing light should be used to check timing, probably can rent one from autozone or someplace like that, have to make sure the basics are ok to move on to the next step in daig.
A stretched timing chain will mess the running of the motor also,
As for the trans[dont know what you got] but most likely there should be a vacuum line running down to a vacuum modulator valve bolted to the case, make sure you have engine vacuum to it and it is not chewed up by some critter.
