Can I-140 be applied by a company without me being an employee of the company.

Yes, it can be filed without being an emloyee of the the company, must intend to hire you full time as per your approved PERM. Rest is company policy

Does filing my spouses EAD application along with L1B/L2 extension has any impact on the L1B extension decision?

EAD can be filed 120 days ahead of expiration so make sure that it does not have more time on it. It will not impact your L-1B extension.

If I stay out of country for one year before I complete my 7 years then can I come back on same L1A visa?

Yes, you can come back on the same L-1A if company wants you to come back on it and you do not voilate any terms of your employment in USA.

I have a work authorization with pending adjustment of status. Can I transfer to another job/company?

If your I-485 Adjustment of Application is pending for more than 180 days, you can change the job under portability rules

Will the immigration officer contact Egypt to see if they were married there?

If USC wants to file Fiance'e visa then he can not marry her in Egypt, must get engaged, come back and file fiance'e petition (I-129F) or after...

Could he come back in US after April if I bring him Green Card in country, in which he will be?

you should make an Infopass appointment on www.uscis.gov and get the passport stamped before leaving the country.

if it is administravely closed, you can file for your EAD

it should not affect your case if you are living together and marriage is in good faith

Can I start working for CompanyB with receipt no. or Should I wait till I get approval and then re-enter US before starting

Your job ended on October 15, 2015, immigration may not give extension of status, you might end up going back to home country or port of entry and...

Do non-profits have to apply to h-1b visa in the month of April as regular companies or are they exempt of timings too?

Non-profit organizations are CAP exempt and can file for H-1B any time.