Do I need to use sterilized jars straight away

Before filling the jars, you should do the following:

• Place the jars (right-side-up) on a rack inside a boiling-water canner
• Fill the canner and jars with water to one inch above the jars
• Boil for 10 min (or more for higher elevations)
• Remove and drain the jars, one at a time

I toss the lids and rings in there as well, since the lids seal best when the rubbery-stuff is softened first anyway.

I have read that some people use their dishwasher's "sanitize" cycle instead, but you should contact the manufacturer (or check the user's guide) to see if it really gets hot enough. I don't know much about using the dishwasher for this purpose; perhaps someone else can elaborate.

If you're looking for great canning instructions, check out the National Center for Home Food Preservation. They will explain how to can safely, botulism-death-free.

Are these bacteria also present in sterilized milk?

If something is sterile, then by definition it does not have any live bacteria in it. That only applies while the milk is sealed in its original sterile container, though.

Can these bacteria be introduced from the air or from the bread [flour]?

Absolutely. There are bacteria and yeast living in the air, flour, and on every surface in your kitchen (including your bread maker). Wild yeast and bacteria in the air and flour are used to make traditional sourdough bread.

Are there other bacteria or toxins that will develop in sterilized milk when exposed to room temperature for a few hours?

I'm not sure how this differs from the above question, so: yes.

Speaking practically, if you are setting the timer for less than 4 hours, I think the risk of getting some sort of illness from this is rather low. The baking process will likely kill the bacteria before they have a chance to produce enough nasty toxins to make you sick. If you refrigerate the milk beforehand, you can even buy yourself a little extra time, since the milk would need to warm up slightly before bacteria could start reproducing in it. I still wouldn't make a habit of this, since there is still some risk of contamination. Leaving milk out on the counter just isn't a good idea, even if it was originally sterile.