Engine still not right after timing set

I appreciate all the detailed feedback. I spoke to my mechanic today and he's waiting on some new plug wires. Apparently, only 4 of them were working correctly he said. Considering I just replaced those wires 2 years ago I'll have to note what brand they were from Jegs so I never buy them again, because that's pretty terrible.

If your headers are not properly sealed at the heads, then they will pull fresh air in, as part of the way they operate. Any unburned fuel in the headers is gonna "explode". This makes a lotta noise in the headers, and COULD make it seem like the engine is not running right. This is worst at low rpm/idle.

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The pops/misfires I'd hear were more prevalent when the engine was under some load.

Once all the wiring is taken care of, if there's further issues I'll definitely bring all this up with him to check out. He seems like a pretty reasonable guy and has been straight forward about what actions he is doing.