After KEGG and GO analysis, how to make tables+phylogenetic trees
I'm going to answer 1+2 because 3 is hard to understand and maybe trivial?

Each of 1+2 seems to be have these sub-tasks:


identify the contigs in your assembly that have the genes of interest.
pull out the gene sequences from the contigs (you should have intermediate tblastx output somewhere with coordinates, if you don't you can just re-blast those contigs).
possibly translate those in silico to protein sequences.
tblastx (gene) or blastp (protein) those gene/protein sequences against whatever db is relevant.
pull sequences for the hits above some threshold for each gene from the db.
perform a multiple sequence alignment for each gene against the hits.
plug the MSA into whatever phylogenetic tool you like. I used phyml a lot back in the day, don't know what the kids like now.
make a visualization of the tree, probably?