Well, you are doing all the right things. And as soon as you see the gilding looking better, then all the little imperfections get amplified. As you already know, metal leaf and even more so gold leaf will copy and accentuate even the smallest blemish on the surface to be gilded.
That's why, to use the old trope, it's preparation, preparation, preparation.
Since it's not a surface blemish on the timber, it's probably something on the gesso layer.
Because you have chosen to use artificial gesso, the range of repairs are a bit limited.
First of all, you don't need to apply a coat of Zinsser sealer.
Just paint on the gesso straight onto the timber.
And don't bother to sand between coats - just get it on as thick and SMOOTHLY as possible. Maybe dilute the gesso a little bit with some water to make it more workable.
Letting it dry off a bit between coats will help.
The next bit is the important bit.
Sand the gesso FLAT with a coarse grit of about 120grit. This is just to create a perfectly flat surface. The next grits which will be higher, are simply to remove the coarse grit scratches and then move to a finer polished surface.
And remember what I said on my previous reply, move up the grits inside multiples of x2.
So its 120 to 180 to 320 to 600.
As you are using a plastic acrylic gesso, you perhaps don't need to seal the surface - but I would.
Paint on a thin coat of French polish/ shellac. Dilute it 50/50 with methylated spirits/ alcohol.
Now go ahead and apply the oil gold size. You mention using a 1 hour size. Move to a 3 hour size for better results.
Remember to paint it on first, then pull as much off as you can using a cotton cloth and paintbrush.
Leave any sort of wet puddle or excess oil behind and that will show through on the gild.
In fact that maybe the source of those strange marks.
Good luck with it all. You will get there in the end.