Tough choice, both have their benefits, 400 obviously faster but lacing the range though still would be reasonably fast with a 1.4 or 1.7 tc. Personally id go for the 600mm for wildlife, chuck a 1.4 on there and you have 840mm of reach to play with which is great for things like small birds where you cant get close. Im lucky enough to have a 200-400 which is superb but sometimes find it a little short at 400mm hence is quite often use the 1.4tc on it, so the 400, i think, would be a little short though it is widely used for sports and is very good at it. There is not that much difference in price to be fair so it would be down to you to decide what is right for your needs, i would strongly suggest that you rent both before stumping up the cash, that way you can put them through thier paces without spending a kings ransom only to find you have made the wrong choice.

Hi, This lens supplied with protection glass for front element and it's removable you can replaced it any time you want.

Yes, the AF-S NIKKOR 600mm f/4G ED VR is fully compatible with Nikon D90.

If AF-s version answer is yes. Unsure if AF-I.

On a mono pod I would leave it on, you will still get some camera movement unless you have extremely steady hands.

Yes

By using the lens hood.

Yes