Sounds like an aggro-range problem. I've had wolves chase me from area to area before, but what you're describing might be an enemy pathfinding issue. Hell, I wouldn't be surprised given how wonky NPC pathfinding is.
You have to face the fact that there will be limitations on the mods due to the game's online component. Anything that is modded beyond what the global server ID Archive has on file will corrupt save data... if given to the Main Pawn. And that's the thing, you'd have to play offline for the rest of the time you have such mods installed. Texture mods are fine because that is all handled client-side. But meshes and the like will likely not be possible unless Capcom makes a serious change to the way the Pawn System operates.