require(raster)

# round resolution to nearest arc second
snap_res <- function(r) {
  round(res(r)*3600)/3600
}

# make sure extent fits cleanly onto a grid
# having its origin at -180, -90
snap_extent <- function(r) {
  origin <- c(-180, -90)

  ll <- origin - round((origin - extent(r)[c(1, 3)])/res(r))*res(r)
  ur <- ll + res(r)*dim(r)[c(2, 1)]

  raster::extent(c(ll[1], ur[1], ll[2], ur[2]))
}

footprint <- raster('footprint.tif')
yield <- raster('yield.tif')

res(footprint) <- snap_res(footprint)
res(yield) <- snap_res(yield)

stopifnot(res(footprint) == res(yield))

extent(footprint) <- snap_extent(footprint)
extent(yield) <- snap_extent(yield)

combined_extent <- merge(extent(footprint), extent(yield))

footprint <- extend(footprint, combined_extent)
yield <- extend(yield, combined_extent)

stk <- stack(footprint, yield)