a suggestion
Not sure if your problem has already been worked out or not, but in case it hasn't, I hope you don't mind if I chime in.
It would seem to me that there has been a breakdown in communications between you (the tenant) and the landlord, likely due in part to the agent.
As it stands, you're both in an untenable position. You aren't comfortable in your own home, and your landlord has a potentially hostile tenant who she likely won't be able to budge for a long time.
Fair enough, the landlord MIGHT be able to get more from someone else, but keep in mind, responsible tenants are EXTREMELY valuable to a landlord. You seem like responsible tenants, so the landlord will likely want to keep you, albeit at a higher price.
Aside from the agent, do you have any friends or acquaintances who might bridge the gap for you? Ideally, you should be able to sit down for a coffee with your landlord and discuss this face to face. Likely your landlord has a different picture of you than you paint. Give him or her the chance to explain things from her point of view, and actually listen. Getting together informally on neutral ground is an extremely underused negotiation tactic.
Explain to him or her that you like the apartment and that you have been paying the rent on time (although it's likely the agent didn't forward that on time). Offer to pay directly and have her take care of the agent. That way the middleman (read: obstacle to progress) is out of the equation.
Explain as well that you have been doing repairs and upgrades, but that there are issues that the landlord needs to address. Not because of you, but because they are damaging her property. Tell her you'd be happy to schedule and supervise the work, and even pay for it providing she'll credit your rent. Remind her that you're serious people and want to help her keep her place looking nice.
As for the rent increase: if she agrees to fix your problems, you form a better working relationship and can have peace in your home, why would you want to move? If you're really paying below market value and the landlord agrees to your reasonable suggestions (note I didn't say demands), I don't see why you shouldn't pay a little more.
Basically, give your landlord every opportunity to save face. Redefine the situation as being both of you wanting the place to look good and be maintained. Explain that you are happy to pay a little more, provided you get what you pay for.
If that doesn't work (and I'm fairly certain it will), request a reasonable time to move out.
Remember: the point is to come to a solution you can both live with. Leave something on the table. Above all, never try to take someone's dignity; it's worth nothing to you and everything to them.
If that doesn't work, well you tried.
This stuff about paying into banco agricula and getting a lawyer etc is a lose/lose for both of you. You will have no peace in your home, both of you will pay lawyers (thereby eating away whatever savings or rent increase you're talking about) and at the end of the day, neither one of you will get what you want. You can fall back on that as a last resort.
Remember, the more you play hardball and back someone into a corner, the more difficult it is to be reasonable afterwards. Be reasonable first and save the heavy ammunition for when it's needed.
Hope this helps.