I’m afraid that does’t rule out a warped head. I too drive a 1998 Civic, and I recently had a similar issue. I noticed my temperature gauge was running a tad higher than usual at stops, but nowhere near the red. I took it to shop after shop to have the cooling system diagnosed (and nobody could find anything wrong), but in the end, I had to bite the bullet and have a new head gasket installed. It turns out the head gasket was bad (deteriorated) and that was the cause of the slight overheating at stops. When the shop sent the head to have it planed, it was slightly (about 1/32 or 2/32 of an inch) warped.
The problem you’re likely facing is that when the head gasket fails in a 6th generation Honda Civic, it doesn’t exhibit the symptoms most mechanics expect from a failed head gasket, and your head gasket might have been either damaged during installation or improperly installed. If you’re able to rule everything else out, and it keeps overheating, it might be time to let this car go or fork out $900 to have a head gasket professionally installed.
Another problem you’re likely facing is that this vehicle is highly susceptible to damage from overheating. My temperature gauge needle got nowhere near the red on the gauge, and yet the head got warped. I just happened to notice the temperature gauge needle, which normally points at the squiggly lines on the gauge, was pointing to the top of the top of the temperature gauge icon.