Hi Mark,
Just found this thread.
We have to presume the Doc drained the fuel tank for four reasons.
1. He is a scientist and would know the fuel would go bad if left in the tank for 70 years.
2. In BTTF II the car spends most of it's time flying which would not be powered by gasoline, so would he have need to have much fuel in the car anyway?
3. In BTTF III when they are at the Drive in Movie, Doc tells Marty he's put fuel in the car. Therefore we can correctly presume it was drained and had none in it during storage
4. Bob G and Rob Z's story line is pretty watertight which makes the whole trilogy stand the test of time. 1885 Doc couldn't use parts off the buried car as they simply had no fuel even if they "borrowed" the metering head.
Also if you question why they didn't fly in BTTF III instead of being pushed by the train, its clearly written into Docs 1885 letter read in 1955, that the lightening bolt damaged the Hover conversion and the car will never fly again.
In 1955 the fuel Doc put in would have been leaded, but by the sound of the engine and the lack of stock tail pipes it had no CAT anyway. Even if it did, 1 random tank of leaded wouldn't have killed the CAT straight away and the engine would have still ran.
Nice question though Mark