The Pokemon that he has are
Shadow Rhydon Lvl46
Shadow Exeggutour Lvl 46
Shadow Articuno Lvl 50 Sig Move. Shadow Chill; Power 75
Shadow Moltres Lvl 50 Sig Move. Shadow Fire; Power 75
Shadow Zapdos Lvl 50 Sig Move. Shadow Bolt; Power 75
Shadow Tauros Lvl 46
You face him after Shadow Lugia.
Have an empty spot in your party and use the Master Ball on Lugia you will snag him without battling him and he will be in your party for the final battle! It worked great for me. The others attacked Lugia with shadow attacks. Of course they were not very effective. While my Lvl 55 Espeon pounded away with Phychic! And so you know you can challenge him anytime afterwards to get his pokemon.
By the way. How are you doing in the Key Lab?