Also after I receive the visa, would I have to return to Japan every 3 years to renew it, like she does?
Wait.
She has a visa, or she is a Japanese? Which is it? (I suspect she is a Peruvian by nationality/passport, but that she has a "specified visa" for "long-term permanent resident". If so, you should confirm that you can actually get a spouse visa, or if it is a dependent visa that you need.)
If you get a work visa or spouse visa, you can leave the country, but to keep the visa status, you will have to buy a reentry permit if you plan to return to Japan under that same visa. Why would you get a work visa, then leave for almost 3 years?
Besides, work visas and spouse visas may be for 1 year or 3 years -- luck of the draw (and you are unlikely to get a 3-year spouse visa right off). Stay outside Japan for longer than that, and you invalidate the visa.
As for needing to come back to Japan to renew (the official word is "extend your status of residence), the following people are authorized to file the paperwork (however, immigration can do whatever it chooses, and may even ignore the following):
1. Applicant;
2. The following persons are authorized to submit application form on behalf of the applicant foreign national:
* A staff member of organization that is run by or employs the foreign national;
* A staff member of organization that trains or educates the foreign national; or
* A nonprofit organization authorized by the competent authorities under the Article 34 of the Civil Code for the purpose of smooth acceptance of foreign nationals;
3. A lawyer or administrative scrivener that gives notice to the director of regional immigration bureau; and
4. A legal representative of the foreign national;* or
* "Legal representative" in this context means a legal representative of an applicant who is younger than 16 years old, is always unable to make sense of his/her surroundings due to mental disorder, or significantly lacks such abilities.
5. The applicant's relative, housemate or other similar person who are regarded as appropriate by the director of regional immigration bureau (if the applicant is not able to visit the regional immigration bureau by himself/herself because of illness or other reasons).
I mentioned the caveat above because of my own experience. I needed a reentry permit. Item #5 is cited as being able to do this for me, so I called to confirm that my Japanese wife could do that. They said flat out "NO!" I would have to come in personally. Another office said she could, but only if I could prove I was sick and unable to go myself.
Your wife may not have to physically go into immigration with you, but how is she going to get her koseki (family register)?