This sounds to me like there may be two problems that are simultaneously affecting your car. Since we are all just guessing at this point, you’d probably be best to start off with the easy tests:
1)
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The shop did find some very minor particles along with what appeared to be water droplets.
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These “minor particles” have a way of accumulating until they become a major nuisance. You might consider replacing the fuel filter element since this can lead to misfiring and fuel starvation. You might also want to run some techron through the system since it sounds like you might not only have dirty fuel but also old fuel which tends to gum up the injection system.
2)
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Finally pulled my plugs, all black.
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Have you checked the CO adjustment with an exhaust gas analyzer? Black plugs means you are running too rich – duh! There is really no easy fix here. You need to run through CMA. Get a copy
here.
Finally, make certain that the throttle valves are synchronized at 3,000 rpm. Varying degrees of air intake can lead to all sorts of misfiring and poor running.
Good luck.