Why didn't you just order it with that stuff? Those are all factory options. Well anyways....
Dual batteries-- make your own "kit" using a quality switch and tinned marine wire. Easy as pie. Just don't forget a battery hold down/box so it doesn't fly away and start a fire.
Transom trim control -- factory plug in harness, get it from your dealer
Underwater LED lighting--
http://www.oceanled.us/home.htmlUpgraded stereo-- Unlimited possibilities. Millions of threads in here. Personally I like Infinity Reference speakers and Kenwood head units. Polk makes awesome marine rated subwoofers (DB series). Just make sure whatever you get, it has Bluetooth