It sounds like you had drain flies, not fruit flies or fungus gnats. Here is the info that I found:

drain flies

I am not endorsing this company, btw, just found the info via web search.

I'm glad you're past this problem, I can imagine how annoying and aggravating it was.

Not that it matters now because what's done is done, but there are mixed opinions about whether the perimeter of a toilet base should be caulked or not. The "do not" view is because should there be a leak or failure of the wax ring (or a more modern equivalent) at the flange, you want any leaking liquid to be visible. With a caulk around the perimeter, it would remain trapped underneath.

If the wax ring is intact and has no gaps, and if the insects were coming from the drain, they wouldn't be able to get through anyway.

Happy days!

Yeah - I actually wound up buying 2 different brands of enzyme drain cleaners, used them several times in ALL the drains. I plan on using it again. At first I used the ammonia method, it didn't work either. And yes I did a LOT of online research and did read some statements that it's not good to do the caulking but we needed an immediate fix and will look into getting the toilet checked out by a professional. We did a lot of the things I mentioned previously several times, not just once, man what a nightmare. DH runs like a deer when anything is mentioned about DIY plumbing, very shocked that he even did these 2 things. He's a journeyman electrician and knows his way around that and a few other things but he has a bad phobia about anything plumbing-related. The gnats were either fruit flies or drain gnats (not drain flies) but they look similar, I tend to lean to the drain gnats though, but they do like vinegar, and they also like Kombucha and beer, too. I used them all 3 in the homemade traps.

Yes the plumbers that did all our work said no caulk around bottom of toilet. It should be able to leak out there. If not you risk holding moisture there and rotting out the subfloor under the toilet.. If caulk is put down there should be a gap left to let liquid seep out. A proper fitted wax ring should take care of the sewer seal. There are other opinions to that of course. We have no caulk.

https://diy.stackexchange.com/questions/68468/are-toilets-supposed-to-be-caulked-to-the-floor

Good discussion with both sides lol.

I did have a toilet leak that had caulk except for the gap and water was squirting out of the gap. Only way I knew it was leaking. That's why we agreed with our plumber not to caulk.

Were they little heart shaped gnats? Bigger than fruit ones, but not as big as a fly?

We've had a few of those in our bathroom too! Now I'm really concerned it'll get worse!

We don't have a sub-floor, it's concrete slab underneath the vinyl flooring we have in the bathrooms. Also yes I looked at all the pictures online, the two that look similar are the fruit fly and the phorid fly, and I suspect it's the phorid fly. The pictures of the drainfly on the link supplied above is not the one. I just wish we knew which of the 2 last things did the job, the grouting or the replacement of the Studor vent. Maybe I should have posted this on the plumbing forum. Too late now, I don't know how to go back and do it after the first post.

It could be none of your solutions solved the problem. Occasionally gnats simply swarm seasonally. Then they mysteriously leave.

Drain flies don't tend to fly out all over the house. Mostly you would see them around the sinks and tub. Gnats don't generally originate in a house. They come in from the outdoors. Spring, warm weather, open windows and here come the gnats. They are often small enough to slip through screens.

But Elmer is right about the toilet,. No way could they come through there unless the seal was compromised. IF that seal is compromised then caulking added a very expensive hindrance to identifying any leaks which could cost you much more than a new seal in the future. Like a whole new damaged subfloor, even concrete can get mold issues, since the leak won't be as apparent with the caulk hiding it.

I believe one of your cleanings may have eliminated the drain fly habitat. It was none of the mechanical fixes.

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