here are some things to help you out. Since I don't have your .tif files just some hints. Have you checked the extent on your raster s? It's the size of the world, with just those columns its cells are extremely large. So you have to add an extent to your raster before resampling it. From your info I did something like this:
# create an extent that includes all your data
e<-extent(-46, -43, -2, -0.6)
# create a raster with that extent, and the number of rows and colums to achive a
# similar resolution as you had before, you might have to do some math here....
# as crs, use the same crs as in your rasters before, from the crs slot
s<-raster(e, nrows=7000, ncols=7800, crs=r1@crs)
# use this raster to reproject your original raster (since your using the same crs,
# resample should work fine
r1<-resample(r1, s, method="ngb")
Happy Holidays, Ben
PS a better way to find your desired extent & resolution:
# dummy extent from your rasters, instead use lapply(raster list, extent)
a<-extent(-45.85728, -43.76855, -2.388705, -0.5181549)
b<-extent(-45.87077, -43.78204, -2.388727, -0.5208711)
c<-extent(-45.81952 ,-43.7173 , -2.405129 ,-0.5154312)
extent_list<-list(a, b, c)
# make a matrix out of it, each column represents a raster, rows the values
extent_list<-lapply(extent_list, as.matrix)
matrix_extent<-matrix(unlist(extent_list), ncol=length(extent_list)
rownames(matrix_extent)<-c("xmin", "ymin", "xmax", "ymax")
# create an extent with the extrem values of your extent
best_extent<-extent(min(matrix_extent[1,]), max(matrix_extent[3,]),
min(matrix_extent[2,]), max(matrix_extent[4,]))
# the range of your extent in degrees
ranges<-apply(as.matrix(best_extent), 1, diff)
# the resolution of your raster (pick one) or add a desired resolution
reso<-res(r1)
# deviding the range by your desired resolution gives you the number of rows and columns
nrow_ncol<-ranges/reso
# create your raster with the following
s<-raster(best_extent, nrows=nrow_ncol[2], ncols=nrow_ncol[1], crs=r1@crs)