Should I apply for Naturalization?

Yes you are eligible for naturalization.. Generally, none of the matters you mention pose a bar to citizenship. Consider working with an...

Can a DUI lead to problems reentering the US?I am on F-1 visa and my DUI case is still pending would this be a problem ?

A DUI can lead to your visa being cancelled and could result in not being permitted to return to the US without first obtaining a new visa.

How long would it take for company/lawyer to receive RFE?

Yes - it often takes that long and possibly longer.

Can I get approved again for DACA if I got a DUI?

With a DUI conviction you will not be permitted t renew DACA.

Yes if the US consulate accepts third country nationals for H1b visa issuance.

Can I extend my J1 visa for the time I spent outside the USA during my academic training?

As my colleague recommends speak with the program responsible for your program.

A DUI may result in your visa being cancelled. If the visa is cancelled you will not be permitted to return without securing a new visa.

Marrying a non US citizen

The principal forms are the I-130 and I-485 assuming she is eligible to adjust status. If you are going to try this on your own use the USCIS...

Can I file a case against my former employer? .

Best to talk with an employment lawyer as this is not an immigration question.

No update after submitting rfe

As my colleagues recommend speak with your attorney. CIS in Cleveland often takes a long time to make a decision after an RFE.