Still sounding to me like it is an ignition-related issue, in terms of the miss.
Your mirror photo above is of the smog pump with rubber broken off on the nipple.
For the EGR valve, you may be able to just replace the gasket at the base, and see if that solves the problem. That is, if the EGR valve is not stuck internally.
Honestly, I would strongly consider just replacing all of the soft bits at the intake manifold and the top end of the engine. That would include all vacuum lines, gaskets, rubber nipples and connectors, black rubber air hoses atop the manifold, Tecalan tube that goes off the ETA, ETA gasket, EGR gasket, ETA rubber boot, rubber smog pump hoses, possibly the rubber donuts that mate the halves of the intake together.....the whole works. You won't regret it and it's a job that could be done in a day, or over a weekend.