I didn't read every post in this thread, but dropping toilet bowl levels are usually caused by the main drain line being partially clogged with solids (mostly from the kitchen sink).

For example, if you add a toilet in your basement (if you have a basement) no plumbing code in the world is going to expect you to install another vent stack in your house for that toilet. That's because sewer gas is smelly, but it's not poisonous, so the worst that can happen is that your bathroom smells like an outhouse.

If you add a toilet in your basement, all you have to do is connect the toilet drain line to the main drain line coming off the bottom of the vent stack. If that main drain line is partially clogged then when you flush the basement toilet, that toilet's drain pipe get's filled with water (cuz of the partial blockage). Now, as that water seeps away past the partial blockage, it creates suction behind it, which in turn sucks the water out of the toilet bowl.

To check to see if this is happening, flush the toilet, and then once the bowl has finished filling, shove a flexible tube through the water passage way of the toilet bowl and blow into that tube to clear it of any water. That way, any partial vaccuum in the drain pipe will be filled by air flowing through the tube.

If the water level doesn't drop with the tube in place, then you know it was a partial vaccuum in that toilet's drain pipe that caused the water level in the bowl to drop, and there wouldn't be a partial vaccuum if there wasn't a blockage of some degree in the drain piping the toilet water flows through.

I don't know what's causing the black marks, but if bleach removes them, then they're organic.

I wouldn't pour muriatic acid into the toilet tank's over flow spout. Not ALL of the rim holes are going to be blocked, and so most of that acid is just going to leak into the bowl. I would use a mirror and dental pick to clear each hole manually. It's awkward, but it's not very difficult.