Well, judging by the amount of dust on the camera lens when you took that last picture, I'd say you were having a tuff time too. But, this is fixable in my view.
1. I don't expect using Henry's is gonna cause a problem, they should both make decent floor leveling compounds.
2. You said: "We painted with big box epoxy 1 part paint."
I've never heard of a 1 part epoxy. So far as I know, all epoxies are two part. You mix the two parts together before applying it to the floor. I've heard of waterborne epoxy paints, which I suppose would qualify as a 1 part epoxy, but I've never used any waterborne epoxy paints.
3. You said: "First - darn those fish eyes in spots."
By "Fish Eyes" do you mean those "bumps" that seem to be evident in the light reflecting off the floor in the second picture?
If so, I think you should take bright light and hold it close to the floor (or rest the light on the floor) to see whether doing that makes them appear to be "bumps".
I can't help but notice a strong similarity between the things under the paint in the second picture and the grey things on the brown floor behind you in the last picture. I expect those grey things are where you patched chips in the concrete floor with the Henrys floor leveler. Did you sand the floor leveler down flush with the floor before painting over it?
Also, floor leveler shrinks as it dries. Consequently, you typically need to apply a second coat of floor leveler to a filled in chip to also fill in the shrinkage of the first coat of floor leveler. I'm concerned that if you didn't do that, the "dip" in the floor leveler at each chip may be what's causing those things under the brown paint in the second picture. If so, this isn't a dire problem. Floor leveler is relatively soft, and you can scrape those things down with a paint scraper to remove both the paint and floor leveler.
No, you don't need a clear coat over top of an epoxy paint. Clear coats are typically used to protect an underylying softer paint from damage. If you're already using an epoxy floor paint, you won't find a harder clear coat to put over it (other than a clear two part epoxy but that shouldn't be necessary). Your epoxy floor paint should be hard and strong enough to stand up well on it's own without a protective coat on top.
There are siliconized acrylic caulks, but I've never heard of a siliconized acrylic paint. There are acrylic paints, which are basically just good quality latex paints. In my view it's not a great idea to put an epoxy clear coat over an acrylic paint on a concrete floor. By doing so, you're relying entirely on the epoxy top coat to provide durability because the acrylic paint underneath is very soft and easily damaged. You'd do better with an oil based polyurethane floor paint, or a coloured two part epoxy floor paint, and neither one would need a protective clear coat on top.
If the floor machine in the last picture is operating, then you're holding it way wrong. The handle is only up like you see it in that picture when you're about to tilt it onto it's wheels for moving it, or when it's in storage. There should have been a large wing nut near the base of the handle that you loosen so that the handle pivots. You pivot the handle downward so the handle bar is somewhere between the top and bottom of the zipper on your shorts. You then just lift the handle and the machine will move one way or lower the handle to make it move the other. I hope you didn't scrub the whole floor with the handle in the upright position the photo shows it in.
Also, what did you use to sand the floor down; a sanding disk on a high productivity pad, a high productivity pad or just a black pad?
I think your best bet now would be to level out those "fish eyes" by putting a bright light on the floor and scraping the paint off them with a paint scraper (the kind with the tungsten carbide blades). The bright light will make them easy to find, and floor leveler is soft, so they should be fairly easy to scrape down flush with the concrete.
Did you add any "additive" to the Henry's floor leveler? If not, then the floor leveler patches should be quite easy to fix up.
Can you get back to me with some of the answers to my questions, and we'll figure out a way to fix this. You've got a lot of "fish eyes" there, but I'd like to get your impression of whether they look more like bumps and depressions when viewed with a bright light shining on them at a sharp angle to exagerate their profile. Place the bright light on the floor or hold it just above the floor and see if the problem is more that the substrate under the paint isn't flat. If you concur, use a paint scraper to scrape down one of those "fish eyes" and see if there happens to be Henrys floor leveler under that spot. I expect the problem isn't that you used Henrys, but rather that the Henrys hasn't been sanded smooth.
Was that a rented floor machine or is it your own? I'm thinking that if you're willing to call that existing paint a write-off, you could simply redo those "fish eyes", and apply another coat of paint over top of everything.
It's too bad you didn't post as you were doing this floor. We could have advised you to apply another coat of floor leveler to fill in shrinkage, and to sand that floor leveler down flush with the concrete before painting. But, we can still fix this. I can't see a way to fix it without messing up the existing chocolate brown paint, tho.