You will have to post pictures or drawings so we can understand exactly what your situation is. You will probably not be able to remove a rusty bolt unless you can see the situation. Use flashlights and mirrors. The best solution is maybe to cut with a hack-saw blade. Takes time and effort. If you cut or grind off with any power tool, it will be very risky. Make sure you replace with special bolts and nuts that will NEVER rust - plastic or brass or something.

The chain from the flapper hooks on at the top. You must unhook it there.

You must turn off the water at the wall, flush, then sponge out the rest of the water inside the tank. Then unscrew the water connection that is leaking, where it goes in the tank. After you take it apart, you can see and understand how it works. Then clean all the threads and put it all back together. Use vaseline if you need to make the threads slide smoothly. Make everything tight, but mostly just finger tight, not too tight or you might break something. This will probably fix the leak. But if any parts are worn out or broke or it still leaks, you will probably have to replace gaskets etc.

You say you see movement in the water “as though someone were blowing water on its surface”. I think this is water trickling into the toilet bowl from the tank. This is caused either by the tank water level being too high, so that there is overflow, or by a leaking flapper. Put dye in the tank water 10 minutes after a flush, and see if the color shows up in the toilet over the next hour. If you have a leak like this, find it and fix it — stop wasting water!

It is great that you want to fix your toilet. And there is plenty of information available. But it is impossible if there is a counter two inches over the toilet! If you own the house, you must remove this counter, so that you can work on the toilet. If you do not own the house, you must get the landlord to fix the counter and the toilet.

Removing the rust, carefully, is good. Then you must stop the rust from growing again. You can do this with paint, or most any kind of goop, like vaseline or oil. Just keep paying attention to those surfaces, and you will find a way to fend off the rust! You really only need to worry about rust on thread surfaces. The rest of the rust is most likely “surface” rust, just cosmetic. You could just lightly brush it and apply a coating of “rust reformer” to harden the rust. If the rust really eats all the way through something vital you have a big problem, but this is not likely to happen. What rusty metal disks are you talking about? They are probably not too important. You might be able to just reform the rust or paint them. Or you could reinforce them with silicone rubber or epoxy or other adhesives or caulks. But be careful not to cover up rust on important things unless you do a good job of curing it — it is much more dangerous to have hidden rust eating away than to have ugly rust where you can see what is happening.

As a temporary measure, you can just turn on the wall valve to let in water to fill the tank to flush the toilet, and then turn off the valve right away to not waste water. This will work, but you can’t go on doing this because you will wear out the shut-off valve on the wall and then have a much bigger problem.

It is very important to understand that you do not need a working water supply and tank to have a usable toilet. You only need the toilet part! You can flush with a bucket of water, that you can fill from anywhere, like the bathtub. This is a fine way to make do for as long as necessary — it is only guests that will think it is very peculiar!