I don't know what the best way is, but you can align the genes separately and then compare the 8 trees using treespace and select the most representative tree yourself or let treespace create it for you based on the input trees. Additionally, this method will tell you if all of the genes point to the same evolutionary history or there was a recombination or horizontal gene transfer. Treespace is easy to use and has great vignettes that walk you through the whole process.

Your option 2) is the way to do it. Trimming the alignment after concatenation is always a good idea.

I would exclude any species that doesn't have at least half the genes, or half the combined sequence length in case there are large differences in gene sizes.