These two days, generally merged as holiday days in most Catholic countries, falls on Saturday and Sunday this year. Each country will be taking it's own decisions if to includes a Friday or a Monday as an additional holiday day. From what I can ascertain, there will be no additional holiday in Peru. All regular archaeological sites and museums should be open for business.
No matter where you are, you will find celebrations on both days, probably more so as they fall on Saturday and Sunday this year. You probably won't find such elaborate and extensive celebrations as those in Mexico and Guatemala. Nevertheless they will still be impressive.
The main cemetery in Lima is El Angel. It is huge and probably somewhat overwhelming. If you want to see true indigenous celebrations you should look to smaller cemeteries in the "Pueblos Jovenes". Try to find someone to go with you and get to Comas or Villa pueblos. Here is a remarkable video of the Villa celebration.
http://www.youtube.com/watch?v=dOOqEo7OZ_w...feature=related You will probably find out much more information as you travel.
Good luck and Feliz Dia de los Muertos.
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