Cleaned wheel, V-brakes are now moaning Yesterday, I cleaned my 5 months old bike using WD-40 Bike HEAVY DUTY DEGREASER and removed some dirt and brake material residue from the wheels. Now my front brakes moan. 

I did go through this question and I did set toe-in to around 2 mm, which helped somewhat. Now it's just moaning, not moaning like an old train braking.  

I also sanded the pad surface a tiny little bit with a 2000 grit sandpaper. The pads are clean and free from any derbies or foreign particles. They still have some 3 mm before the wear indicator. 

The wear on the pads looks mostly even, but there's a bit of unevenness due to the wheel rim wear indicator, but I checked and those points are making good contact with the interior of the indicator. 

I'm not really sure what to do now. Most of the searches provide me either with the toe-in solution or give results for disc brakes.
Do NOT use WD-40 of any kind on your rims if you use rim brakes. WD-40 leaves a residue. If you have contaminated your rims, clean them off with rubbing alchohol. Once you do that, it'll be like starting with new brakes, so they will take a little brake in to get dirt and rubber re-imbedded in your rims. If the pads have been contaminated with WD-40, and it sounds like they have, replace them. Pads are cheap.