@Jayde: If you're still reading this topic regularly, I may have figured out what was wrong with your self-trading attempt.
When I downloaded process explorer, I had to enable the display of the lower pane found in the view menu. Apparently you can just hit control L to do this as well, but if you want to ensure that it's on you can check it in the menues.
Also, I haven't tested it with jaws, but if you're using NVDA and you're in a part of the window that says pane, that's actually the list of processes that doesn't speak. I think it's just blank for JAWS. If you tab and you hear list view, that's where the handles for that process will show up.
So if you go to the pane or blank part of the window and type RPG, you should be on RPG.exe. You can press enter to confirm this and escape to get out of the process properties. If it doesn't show properties for RPG.exe, keep pressing the keys for RPG until it shows up properly. Then tab over and you'll be in the process handles, which both screen readers actually read. Then the walkthrough you were given works for the most part. It's a little unwieldly since there are quite a few mutant processes, at least on my machine, but if you hit s and start from session, going up, you should find mutant bgt manamon. Press delete on it and click yes, and you can now run multiple instances of Manamon.
Host a room in one instance, join room and type localhost in the other and you're good to trade with yourself.
One other thing I discovered that's potentially a touch more risky is that you can trade between saves as well. If you load up a save from one game, then while that save is loaded, delete data.dat and replace it with a data.dat from another game, you can load the other save up in another instance. This lets you trade starters and such without having to rely on other players for anything.
I think Enes may have discovered this before me, for all I know there's a walkthrough on doing it somewhere. But there ya go.