Does USCIS issue RFE or deny H1B visa extension if there was an arrest and criminal record? It depends on the nature of the crime and whether...

Any person having constant problems with alcohol or other substances, will have some hurdles with visa application.

It will be in your interest to purchase health insurance for your parents and provide evidence of coverage when seeking extension.

An H-1B employer is required to keep public access file for inspection. So long as the requirements are met, an employer can file.

Pending charge may not adversely affect a person's stay in the U.S. However for newer applications, it will depend on whether you are convicted by...

Employer can initiate GC process. You don't seem to be eligible for H-1B yet as you have not stayed abroad for one full year.

H4 work in US and outside US? Yes, only if you are authorized to work in the U.S. and have an Employment Authorization Document (EAD)

If the position for which the PERM is being processed does not exist or they don't need to hire for that position, the PERM will fall apart.

Can I apply for her I-130 and I-145 jointly ? You will need your naturalization certificate to file for your wife.

Depending on the reason for not seeking the extension in a timely manner, you could either apply for visa abroad or talk to an attorney to consider...