Hello Xfire fun-seekers:
Two questions:
1) Did I just not drive it far enough to fully charge the battery or might there be something wrong with the alternator? I don't think there were any warning lights.

2) Would the dead (the clock stopped) but not removed battery cause problems and if yes would that be screwing up its ability to fully charge the battery?

Details:
This is a fabulous resource but I cannot find anyone asking my two questions.

I know that removing the battery can screw with our babies (computer issues?) but what happens if the battery is just run down to nothing (sitting for many months with tender not connected).

We started my 2004 coupe with a boost and ran it gently for awhile then another 50 kms (30 miles) at about 80 kms per hour (30 mph) and it seemed to be running normally.

But, when I got back, the battery was charged enough to turn on the lights and all but not enough to start the car. Before I turned off the car, I noticed that the exterior running lights and instrument panel lights were flickering. The car was covered with a dust cover in an underground garage for several months. I wonder if the alternator was affected by rising damp.

Any guidance you can provide is most welcome.
Spring is here, finally, and I am looking forward to getting my baby back on the road.

Thanks all!
Crossfire Maggie