Having had lots of battery/charging system problems over the years, I sympathize.
There is a fairly common alternator problem that can lead to a continuous battery drain condition with the engine shut off. I've had this same thing happen to me on at least 2 different Ford cars for certain, and know of it happening to other people as well. In my case, after the first experience, I remembered what to look for. It was a simple part in the alternator that was replaced by the local starter/alternator shop and the problem was solved. I'm thinking that it was the diode array itself, but it's been a long while since the last incident.
If I remember the charging scenario correctly, if ONLY one of 3 diodes in an array burns out, and the other 2 are still working, then the other 2 remaining ones have to work much harder to attempt to keep the battery fully charged. This may be part of what you are smelling.
The low voltage only being present at 1000 engine RPM or below dovetails nicely with this theory. Especially if you weren't running a heavy electrical load from power hungry accessories, which would make the part time undercharging more obvious and not go away until the engine was at a higher rpm.
Passing on a tip from the alternator shop:
To see if this is what is actually draining your battery, try disconnecting the plug to the alternator over night, and check the battery voltage in the morning before trying to start the engine. Then leave the alternator connected over night the next night and compare the 2 readings.
If you have an intermittant problem with the part just starting to fail in the alternator, it may take a while before the problem surfaces again. This is what made it take a while to figure out on one of my cars. It didn't happen every day, but only occasionally at first, and then more and more frequently.
Something simple that gets overlooked in seaching for a charging related problem is poor electrical grounds, like from a broken or deteriorated wire that appears ok from the outside, or from a corroded terminal or an insufficient electrical contact due to dirt or rust. Check yours, and clean or replace any that may be questionable.
One more thing, an alternators' output is dependent upon the ACTUAL speed at which the alternator itself is revolving, and is NOT completely dependent on the engines' speed, so if for some reason you have an incorrectly sized pulley on the alternator itself OR on the pulley that is driving that one, the alternator can be spinning at a VERY different speed than it should be, and it's output at any given engine RPM may be way out of spec as a result. A more common reason for having a SLOWLY discharging battery (like over a week, BUT with the car being started and driven each day for example) is simply having too low of an idle speed setting.