I searched around a bit.
This .exe can be decompiled with ExtractData. (nevermind this program, there's an alternative included below)
From what I can tell, the text seems to be in the "scenario" folder in .ks files, which can be edited with notepad.
Not sure yet how to get everything put back together though >_>
EDIT: Here's what I've found so far. The exe is in a format that merges an executable and an archive (archive.xp3) into one file. A program called kiri_sm.exe can split and merge these files. A program called kikiriki.exe can extract and compile .xp3 archives. Here's a package with these programs.
http://www.mediafire.com/?ko0jww4ozwokiri_sm.exe -e gyakuten_touhou.exe
Splits gyakuten_touhou.exe into _detach.exe and archive.xp3
kikiriki.exe -i archive.xp3 -o gyakuten
Extracts all files from archive.xp3 and places them in a folder titled "gyakuten"
kikiriki.exe -c -i gyakuten -o archiveE.xp3
Compiles all files in the "gyakuten" folder into archiveE.xp3
kiri_sm.exe -m _detach.exe archiveE.xp3 gyakuten_touhouE.exe
Merges _detach.exe and archiveE.xp3 into gyakutek_touhouE.exe
That's what I have to offer on the subject :P