1) We don't know how can we get this court order now
A suit for declaring the adoption is to be filed before the concerned court. Take the help of a lawyer who guide you to file a suit for this purpose.
2) Is it possible to register the adoption deed now
Instead of registering the adoption deed at this stage (this may be barred by limitation),
better file a declaration suit to declare the adoption as legally valid owing to the present circumstance and describe the circumstance under which you approached the court with this suit.
3) Even if its possible to get the court order now, we are not having any proof i.e death certificate of the biological father
You have to somehow get the proof or else an affidavit by the spouse of the deceased duly authenticated by the revenue officials within the territory shall be a supporting document for this purpose.
4) My husband is using name and surname of his step father every where (in PAN, Passport, LC ) except birth certificate. He is living outside India since year almost 10 years and We have never faced any issue before. Was it legal to use name of his stepfather without registration of the adoption deed or a court order.
It cannot be said to be illegal to use the name of his stepfather, but it may not tally while compared with other documents and may lose its authenticity especially in the absence of a valid adoption deed.