Via a flight abroad is probably OK. Take your EDU visa documents with you when you fly in case you get asked at immigration the reason for your entry why you are coming back - coming back to go to school.
A 90 day visa means that the visa is valid for entry up to 90 days after it is put into your passport. IF you do not enter within that time the visa expires and you need to get a new one before you can enter.
.
The allowed period of stay is 60 days.
.
This can usually be extended once for 30 days more at a cost of 1900 baht at the nearest immigration office.
It is YOU swearing an affadavit under oath that the document is true under penalty of perjury.
.
I swear under oath that the marriage certificate is a true and authentic document and that we are legally married. This is sworn in front of a consular officer.
If you have a marriage certificate then get it certified as true (affidavitit) at the local Peru embassy and get an official translation to Thai. Then take that to the MFA in Chengwattana to get legalized for use in Thailand.
You'd need the actual work permit to turn in cancel the work permit.
.
If the employer has already canceled and returned the work permit then you need your passport to get the letter from the labor office.
.
If the employer did not have the work permit (it was in your possession) then it is not canceled (hence the reason they do not have the letter to give you).
.
You can also make sure that they have actually canceled it and not just told you that they canceled it (happens far too often).