1 I'm not certain what the light novels say, but if they agree there is a cheap retcon in universe.  I suspect the novels say otherwise.

The more expensive one is that the computer did the scheduling, and for most of the experiment, they killed about 30 a day. After the various bits of sabotage, they slowed the experiment down to one a day. Or the computer wanted to have a period with that spacing for some reason.

2
That had bugged me too, so I concluded that he couldn't have been limited to one per day, at the beginning at the very least. The first experiments were conducted in a closed indoor environment that would have taken Accelerator less than 5 minutes to kill a Misaka, so it's conceivable that they could run multiple experiments in one day.  Plus, the first Misakas hadn't learned much yet from their network on fighting Accelerator, so they would be easy fodder (even though later Misakas are still relatively easy fodder.)

But still, killing 50 Misakas per day every 5 minutes would take 4 or 5 hours per day, even without allowing for experiment prep time. You'd have to do about 50 or so per day to get anywhere near 10,000 Misakas in one or two years. I don't remember if they actually said it was one Misaka per day, or if I'd just assumed that.

3 If you know your history, you know that 250 a day is feasible for one man with a support organization.

4 The most prolific executioner in history, Vasili Blokhin, personally executed 7,000 prisoners over 28 days during the Katyn Forest Massacre. He started out with a quota of 300 per day.

5 You know, now that you pointed that out, I feel kind of silly not to have realized it. And this is from an author who goes to decent lengths to match the time lines between the two series.

6 Somewhere in the background of the LN, it's explained that the first 9000 or so of the Misaka Sisters were killed in very, very large combat rooms.  We see one of these when 9982 is introduced.    It's how they got up to that number so quickly.

They still managed to go from 9982 to 10032 in 20ish days?  There's some scheduling issues to work out, obviously.