In retrospect Zil what level did you take the boss of 16F at? It's where I'm stuck currently.
Unfortunately reaching levels of 600+ in the post-game has caused me lose any concept of what levels should be during the main game. So basically, I don't remember what level I was. The 16 floor boss is Yukari right? As I recall, I beat her on my first try with no problems, so again, I don't really remember the strategy I used, since I spent no time on her. My general strategy for bosses was to keep my defence buffed by Reimu, keep my speed buffed by Sakuya, and have Cirno slow and paralyze when possible. My tanks were Remi and Meiling, no Tenshi. No single target healers either. My only offensive buffers were Ran and Kaguya. I also had Alice for debuffs and because she's just a sturdy character. Nukes were Patchy, Nitori, and maybe Suwako or Marisa or someone. I think that was my team. Can't say if this is an ideal build, it's just what used when I went through the game, and like I said, I never had any problems. Only one that ever gave me trouble was Eintei group, but that was a matter of strategy, not levels.
About the skill distribution, I'm not sure if increasing elemental affinity is important at that point, I don't remember, but as a general rule you should be sure you use them to improve the characters strengths rather than trying to compensate for weaknesses (Exept for when boosting affinities. In that case boost weaknesses.) and never put anything on evade obviously. Also, and I don't know if I started doing this there or later, but I found that the best use of equipment was increase status resistences. Making characters like Reimu, Meiling, and Remilia immune to ailments became pretty important as some point.