Hi kendo, and welcome to LandyZone.
I'm surprised you haven't found all the info you need - perhaps you search a bit more.
Anyway here are my responses to your queries.
I'd get the stainless by-pass as some the black coated jobs have had the coating peel off and rust.
They usually come with a cork gasket and you can leave the original 'blade type rubber one in place too.
If you're fitting a by-pass the only bit to clean is the 'engine bit' which is the inlet ducting. Mine wasn't too bad so (although the EGR was) and I just scraped it out with a tea-spoon and wiped it all with a petrol-soaked cloth. Some folks have taken it off and used everything from Mr Muscle to putting it in the dish-washer.
The 'duck noise' is the vacuum in the actuating pipe making strange sounds when you switch off and the vacuum fades away. Some folks get others perhaps can't hear it. There is a thread explaining where to de-activate the pipe farther back nearer the vacuum source.
A Synergy is a completely separate thing - its a tuning box especially designed for the BMW M47R to give more torque and power. Link here:
Tuning-diesels for synergy tuning modules.
I suggest you spend a while more reading up then get back if you need more info.
Oh, and check out pcv / oil separator too - it's important.
Singvogel.