You will get varying opinions on this, but for high gravity beers like what you are proposing, I like to pitch close to the .75 million cells per milliliter per degree Plato metric. That would put you in the vicinity of 200 billion cells for your 3 gallon batch.
I tend to make my starters around 1.040. For a one liter starter, that would require 3.8 oz. of DME.
You could pitch the entire starter at high krausen; try to crash the starter at high krausen, wait for the yeast to sediment, decant, and pitch just the slurry; or wait until the starter has fermented out, crash, decant, and pitch just the slurry. This is is also something you will get varying opinions about; you're going to have to make your own decision.
If you choose to decant, you will be able to see the liquid clear as the yeast begins to fall out of suspension. I try to give the yeast two days to sediment, but I've decanted and pitched after 24 hours with good results.
Yes, you can grow more yeast if you make a larger starter (and there is sufficient oxygen and nutrients).
I think it is a good idea to use yeast nutrient in starters.
I don't know the answer to your question about chloramines as I typically decant my starters and don't worry about treating them.
Do you have a means of oxygenating or aerating your starter? If so, you should use it. If not, you can try the method of aerating by shaking (search "shaken not stirred" on this forum), but you'll want more headspace than you'll get with your 2 liter flask (a gallon glass jug would be better, and you can probably get one for a few bucks at the grocery store).
You are also going to want to aerate or oxygenate your wort prior to (or just after) pitching the yeast.