Change the name of the native currency
native in the Horizon server response, but you can name it as you like in the interface. I guess that if you are going to create a separate chain, you'll create a custom client as well, so this shouldn't be a problem.
Change the number of native currency created in the first block to 1000
When you create a private network, the genesis account receives 100000000000 native tokens and you can regulate total XLM supply by burning unneeded tokens or sending them to the time-locked/mulitsig-locked escrow accounts.
Change the number of decimal of the native currency to 2
On the protocol level all amounts are stored as Int64 values. It's you choice how to interpret them on the client side. You can get the precision you need by dividing the raw value by 100.
Be able to create and burn native currency as needed.
This is not supported
Change the transactions fees
You can set the base fee amount during the network upgrade.