Differential gene expression analysis between species
It depends on what type of data you have, really. There are methods developed solely for quantifying relative expression based on count data, such as using edgeR or limma-voom. 

You don't need to correct for gene length to estimate fold-changes of relative expression, what you need to do is normalise by library size first (and in the process obtain log2 ((counts + 0.5)/1e+06) and then, following quantile normalisation, you can just calculate mouse - human or human - mouse to give you an estimate of fold change. 

I still would recommend using something a bit more sophisticated like limma-voom for this task, though, because that also will enable you to get stuff like false-discovery rates for your fold changes.