Does filling separately affect my naturalization interview?

No this should not be a basis for denial of your case.

Yes contact USCIS to request a duplicate RFE be sent.

I sent I for my green card replacement Can I travel to Guadalajara Mex while I wait for my biometrics appnt ?

You should obtain a I551 stamp prior to traveling with copy of receipt notice.

You should use the Avvo search tool to find an experienced attorney suitable for your needs. Good luck!

Depends on what is being requested. Consult with an attorney for review of RFE.

Same Sex Marriage and marriage based Green Card Application

There are options for adjustment of status but her intention cannot be to enter on a tourist visa to do so. Consult with an attorney for guidance.

Adjustment of status -i485?

If this RFE is based on previous marriage based adjustment case, you do not need to respond but may notify USCIS re: status of your marriage.

How does a fourth waiver end for a person?

Please elaborate your question as it is not clear.

Is it possible to enter US with tourist visa?

Your spouse can petition for you through consular processing. Consult with an attorney for guidance.

Do I have to apply for green card renewal in the period waiting for citizenship renewal

No this is not required unless you need to travel outside of the US.