I beat poison 2nd gym with most of my team in tact. I caught a Cubone outside the gym and replaced Noibat with it for the battle after I evolved it into a Marrowak.
The second gym was pretty tough. I lead off with Meowstic and Gourgeist to finished off Nidoqueen, Gengar, and Tentacruel before they went down. After that I relied on my own Nidoqueen, Arcanine, and Marrowak to deal with with the rest of her team. The fact that Nidoqueen was as bulky as she was and had Body Slam and was able to paralizes off made the difference. At the end it came down to a Fresh Greninja against a Full Hitpoint, but Paralized Drapion (damn you ultra potions!) to see he could get the knock-out. I got 4 hits with water shuriken first round, Drapion was Paralyzed, and then I got 5 hits with Water Shuriken to finish it off.
Nidoqueen has Earth Power now, which is nice, and I gave her Sludge Wave, she learned Earth Power, so i changed Nidoqueen over to using her secret ability. Noibat is back on the team and I'm currently trying to level him up so he can finally evolve. I've been carrying him around in since I caught it at level 7, so it's feels good to see it get close.
I also figured out how to do the mystery egg event. I missed the key to the warehouse and didn't know how to rescue the daycare couple, but once I looked up how to find it I did the mystery egg. I got a female Vulpix. I might breed it later for a better one. It does have drought, but it also has 0 Defence IVs, and a -Defense + Speed nature. So I think she just dies to everything if I put her in battle.
I also went back to the where i ran into strength puzzels earlier, and got a Tepig! I think I might replace My Arcanine, Lassie, with an Emboar at some point, since I've never played with Emboar before it sounds fun. I also got a -s.atk +atk nature so, it looks really solid as a bulky Physical sweeper, and the IV spread is pretty good.