No. You are getting more not less than certified.

H1B Actual Salary is around 40% Higher than LCA. would that be concern for my H1 extension and stamping ?

No. You are getting more not less than certified.

Conformation about calculation of physical presence.

You need to be in the USA for half of the statutory eligibility required period.

Afrer the refusal of waiver I-601 for immigrant visa, can I qualify for non immigrant visa and what are the chances?

You can try the no immigrant visa waiver.

What to fill 864 and 864a... ? Help petition for me by my wife ...

Joint sponsor and needs to file a separate I 864 indicating so.

I currently have DACA how can I get a residency?

Same immigration law applies. There is no sexual path to residency for DACA holders.

I-140 RFE Replied regular process. Can I Initiate Premium Now?

Employer can do that at any time if in the opinion of their lawyer it is advisable.

Apply EAD (I-765) while spouse's H1 and applicants H4 extension is in process

I would wait until your have been granted the extension before applying but if you do before it could save time.

Immigration Issue

You should engage an immigration lawyer as my colleagues indicated.

Is unemployment allowed during cap-gap after H1B was approved?

It should be. Not working at all is allowed during gap cap