BlackShark

When you update PKHeX make sure to update your plugins as well, they are outdated.

Before Gen 5 the nature was not stored in the Pokemon data, it was determined by the PID. So it's technically impossible to only change one of them.

The Masuda method was introduced in Gen 6. In previous generations having a foreign Ditto won't change anything.

Start a new save and import the Gen 5 Living Dex pcdata.bin from here. It has all Pokemon but on different levels. Alternatively you could use the ALM plugin and generate your own Living Dex mons. All will be level 100. https://github.com/santacrab2/PKHeX-Plugins/releases/latest

No, just do it on your 3DS.

Read the first post.

Remove the last 4 bytes from the save and it will load. Pokemon Red.sav

Use .GroundTile=

There is only one RTC. If the berries are fixed everything else should be fixed as well. Do you have a save where this is not the case?

Tools > Data > Encounter Database

The error message told you what the issue is. There is no data in your file.

Try this for your fake cart. The other save is ok.

Done. What Asia81 meant in their post above is this tool from suloku, has nothing to do with PKHeX. Pokemon - Emerald Version (USA, Europe).sav