Thanks for the logs, and testing. From what I can tell there's a few errors in the logs.
The first set seem to be crafting recipe conflicts:
Code:
14:50:45 ERROR Json Assets Exception injecting crafting recipe for Hero Elixir: System.NullReferenceException: Object reference not set to an instance of an object.
at JsonAssets.Mod.ResolveObjectId(Object data) in C:\Programming\StardewValley\ModSource\JsonAssets\Mod.cs:line 1692
at JsonAssets.Data.ObjectRecipe.GetRecipeString(ObjectData parent) in C:\Programming\StardewValley\ModSource\JsonAssets\Data\ObjectRecipe.cs:line 34
at JsonAssets.Framework.ContentInjector1.InjectDataCraftingRecipes(IAssetData asset) in C:\Programming\StardewValley\ModSource\JsonAssets\Framework\ContentInjector1.cs:line 165
14:50:45 TRACE SMAPI Json Assets edited Data/CraftingRecipes.
14:50:45 TRACE SMAPI Everlasting Baits And Unbreakable Tackles Mod edited Data/CraftingRecipes.
14:50:45 ERROR Raised Garden Beds Mod crashed when editing asset 'Data/CraftingRecipes', which may cause errors in-game. Error details:
NullReferenceException: Object reference not set to an instance of an object.
at StardewValley.Utility.fuzzyItemSearch(String query, Int32 stack_count) in stardewvalley\Farmer\Farmer\Utility.cs:line 359
at RaisedGardenBeds.ItemDefinition.ParseRecipeIngredients(ItemDefinition data) in E:\Dev\Projects\SDV\Projects\RaisedGardenBeds\RaisedGardenBeds\ItemDefinition.cs:line 102
at RaisedGardenBeds.AssetManager.Edit[T](IAssetData asset) in E:\Dev\Projects\SDV\Projects\RaisedGardenBeds\RaisedGardenBeds\AssetManager.cs:line 198
at StardewModdingAPI.Framework.ContentManagers.GameContentManager.ApplyEditors[T](IAssetInfo info, IAssetData asset) in SMAPI\Framework\ContentManagers\GameContentManager.cs:line 224
14:50:56 TRACE SMAPI Json Assets edited Data/CraftingRecipes.
18:58:57 DEBUG Better Crafting [RecipeManager] Loaded 87 cooking recipes and 204 crafting recipes.
Seems to be the ones from SDV Expanded, and Raised Garden Beds that are specifically in error. Though, it's possible there may be conflict with Better Crafting as well.
The other big error I see that occurs in your 2nd log is this:
Code:
20:03:17 WARN Deep Woods BeforeSave event was called twice in a row. Ignoring second call.
20:03:25 ERROR SMAPI An error occurred in the overridden update loop: InvalidOperationException: There was an error generating the XML document.
---> InvalidOperationException: The type DeepWoodsMod.DeepWoods was not expected. Use the XmlInclude or SoapInclude attribute to specify types that are not known statically.
at Microsoft.Xml.Serialization.GeneratedAssembly.XmlSerializationWriterSaveGame.Write188_GameLocation_PatchedBy<Platonymous.PyTK.Rev>(XmlSerializationWriterSaveGame this, String n, String ns, GameLocation o, Boolean isNullable, Boolean needType)
at Microsoft.Xml.Serialization.GeneratedAssembly.XmlSerializationWriterSaveGame.Write236_SaveGame_PatchedBy<Platonymous.PyTK.Rev>(XmlSerializationWriterSaveGame this, String n, String ns, SaveGame o, Boolean isNullable, Boolean needType)
at Microsoft.Xml.Serialization.GeneratedAssembly.XmlSerializationWriterSaveGame.Write237_SaveGame(Object o)
--- End of inner exception stack trace ---
at System.Xml.Serialization.XmlSerializer.Serialize(XmlWriter xmlWriter, Object o, XmlSerializerNamespaces namespaces, String encodingStyle, String id)
at SpaceCore.Patches.SaveGamePatcher.SerializeProxy(XmlSerializer serializer, XmlWriter origWriter, Object obj) in C:\Programming\StardewValley\ModSource\SpaceCore\Patches\SaveGamePatcher.cs:line 401
at StardewValley.SaveGame+<getSaveEnumerator>d__90.MoveNext_PatchedBy<spacechase0.SpaceCore>(<getSaveEnumerator>d__90 this)
at StardewValley.SaveGame.Save()+MoveNext()
at StardewValley.Menus.SaveGameMenu.update_PatchedBy<spacechase0.SpaceCore>(SaveGameMenu this, GameTime time)
at StardewValley.Menus.ShippingMenu.update(GameTime time)
at StardewValley.Game1._update(GameTime gameTime)
at StardewValley.Game1.Update(GameTime gameTime)
at StardewModdingAPI.Framework.SCore.OnPlayerInstanceUpdating(SGame instance, GameTime gameTime, Action runUpdate) in SMAPI\Framework\SCore.cs:line 712
Seems PyTK, and SpaceCore both work on the save data. In this case PyTK crashes first when encountering DeepWoods data.
---
You may want to try removing a couple of the aforementioned mods, and test further.
I'd start with trying to remove Raised Garden Beds or Better Crafting on the recipe side of things.
And, removing DeepWoods on the save side of stuff. As PyTK is a core framework mod.
Either way there will be a few errors as SMAPI cleans things up. But, give that a try.