If you can get something with Fire Pledge (Monferno) or Flame Burst (Numel or something), it will change Shelly's Field to a burning field, which will not only get rid of Struggle Bug's boost, but also increase Fire type moves' damage and hurt any grounded non-Fire types. Just not when it's raining. Probably get rid of Noibat; it's useless till it evolves.
If you join the Magma Gang (go to the Magma Alley in North Obsidia Ward), do the mission at night, you can get a Water Stone. But if you already joined the Aqua Gang, you'll get a Fire Stone instead, sadly.
For Yanmega, I Paralyzed it, so my Pokemon could actually outspeed it, and then took it down with a barrage of super effective hits.
Your team seems fine for now, but for the things you're asking about:
- You don't get Mienfoo a bit later on, so keep Toxicroak for now. (I personally don't know how great it is though.) Or you could replace it with another Fighting type like Scrafty?
- For Blissey, it has great HP and Special Defense and all, but it doesn't get too many great attacks. If you breed Toxic on it by using E12 (check the Breeding Guide for a link), perhaps it could be a good stall Pokemon, although I don't use stall due to it taking so long.
- Crobat is pretty good, tbh, but I don't know about the double Poison type. If you do replace Noctowl, maybe get rid of Toxicroak, since I personally think Crobat > Toxicroak.
- Granbull is kinda nice to deal with physical attackers, due to Intimidate and Charm, but its Speed is terrible, like you mentioned. But it can get things like Close Combat by breeding (which I don't really do but I dunno about you), if you are interested.
- idk about Cacturne, sorry.
Still, somebody like Luna or Etesian might have better advice than me, since I don't really breed much or anything, but these are just my opinions.