OK, let's say Ol' Almar Zamasee here wants to produce several items (let's say... 3, a Snowcone, a Baseball Bat and a Doorknob)

Almar assigns all three Datacards to one Factory, he retools the factory to produce Snowcones and starts production on 14 Batches of Snowcones, expecting a warm summer on Dantooine, he then continues to Retool the Factory to produce Baseball Bats and adds them to the production line as well... what will happen now? Will production on the Snowcones cease or will they be produced without problems? will they be removed from the queue or will I have to do that manually?

I'm asking this because the rules pages aren't clear on this and I was wondering why I can't retool a factory for more than one item since honestly... one square equals 200kms... a Factory is 5x5 Squares... which equals 1000x1000 kms... which is 1,000,000 km^2... That is one big Factory, I would imagine it to be big enough to take one more than one item, maybe three at the same time... will this be enabled in the future?

If Almar has a factory tooled for baseball bats, then he can produce baseball bats.
Almar then has to wait for the baseball bats to finish before he can manually give an order to retool, after which he can manually add the snowcones.

when producing Items, I have to give a number of how many NPCs I want to use, after production on those iTems has finished, will they be available for the next item in Queue?

so, I use Mr. Jones for the first production round, as well as the second, or will those I selected be "Set apart" for the rest of production?

Of course uhm...mr Jones...is.
You only work on one project at a time, all NPCs are available.