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1. Upgrade the stock (Garrett TD04) turbo charger with a bigger one ? If yes I need the type of the bigger turbo that recommended for 4D56; or/and

This will certainly increase output, but these engines are not renowned for handling increased boost very well. Expect reliability issues.
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2. Porting & Polish the valve, cylinder; or/and
Not worth it. Polishing and porting is for high revving engines.
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3. Upgrade the exhaust; or/and
This gives some improvement.
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4. Install Water Methanol Injection (Snow Performance); or/and
Dunno.
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5. Can I change the head with Common Rail DI-D ?
I doubt it, unless you add all the electronic bits.
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6. My 4D56T came with mechanical injection, can it change with electronic injection so I can use Dastek unichip ?

No, there is no ECU to re-map.

Summary: The 4d56T is a hard worker. If you want a performer, get a later generation TD or a petrol engine. Diesels are not as easy to "upgrade" as petrols.

Don't ascribe to malice anything that can be adequately explained as stupidity!
Pajero LWB Gen1 3.2 Di-D TD Engine
33" Bridgestone D694s
2" Lift
Front Runner Rack