I've been seeing a lot of comments about PGE. So I'll just post what I know about that.
A.
Never use the Pokemon Editor tool. The problem is that it wigs out whenever you even mention the Fairy-Type around it because it has no support for such. Even if you shift every Pokemon with Fairy to another type it might screw things up, there was a problem one or two patch versions ago caused by PGE.
Use G3T instead. It supports more in it's Pokemon and Move editors anyway (only cry pointing and TM/HM/Tutor learnsets are missing), and the item editor is useful for TMs when it comes to convenience with the Move editor (as Item Manager crashes when you point it to TMs that have new moves). The thing about the G3T INI? It's for one version older and doesn't have the sound data marked. This is okay and it works just as good, you just won't be able to set if something is sound based or not (I know this from experience, I wrote it before the G3T update and I really have no idea where that data actually is. If anyone knows that I could write it up and upload it for you, but for now all you need to do is tell it to continue).
B. The modules that don't read off of types or moves? They work. If it doesn't make sure that
1. You have the ROM name set to BPRE. Most other tools with specific support use the MrDS name, so keep that in mind.
2. Compare it and the G3HS INI files as for a lot of it they use the same data. If something's different, copy the information from the G3HS file and transplant it.
As for G3HS... I really don't know as I haven't had any use for it since the last patch. So I can't really tell you if it's a problem with this patch only or if it's human error.
You can use
this to edit the trade data, unfortunately I don't think there are any other tools for it though.
This is the best way to do it. Trader Advanced can do this too, but there are two problems there:
1. It's been known to accidentally screw up the data if you're not careful either way (it'll let you know if that happens), so make a backup first.
2. It doesn't recognize an expanded ability table, so if you want to edit a trade with a new ability you'll have to edit the ability to an original temporarily. Don't worry too much; just set it to the ability number and reset the new ability back. It'll work automagically.