It’s impossible to say with any certainty what’s going on without car in hand but based on the appearance of the cylinder head, water pump, and the description of a lot of gooey gray sealant protruding between various parts this does not come across very well as a quality repair.
Seeing gaskets with globs of RTV sealant (gray, black, red, or whatever) would make me a bit antsy as that is not necessary, not needed, and not very professional.
Some cars of the 1990’s still had idle rpm adjustment screws, sometimes called idle air-bleed screws. On the 1998, probably not, but if yours has one, and its been adjusted out of its nominal range, that can cause idle surging. Usually though it is caused by some combination of air leaks and sticking idle air control servos.
My 1997 Mazda Protege still had an idle screw
I wouldn’t rule it out that a 1998 Civic might have one
yeah it does have one. i can tell the cable was re-ajdusted. i couldn’t find the screw myself back when i was looking for cheap easy fix, but it’s suppose to have one. from what i read if they messed with that an that’s the reason for the idle issue, then i need to reset the computer an o an “idle relearn” if they didn’t already do it.
They should have disconnected the battery before removing the head and that will reset the computer. The computer has to go through a relearn process now and that may explain the hunting idle. Give it about three days to settle down, then if it doesn’t, take it back.