I ended up fumbling with the manifest thing enough to understand that the tutorial I was following was only half necessary.
Here is what I did (after getting it wrong a few times):
1. Changed registry key to allow for external manifests.
2. Accessed the programs real manifest using Resource Hacker
3. Copy and pasted real manifest into notepad.
4. Changed <dpiAware>true</dpiAware> to <dpiAware>false</dpiAware>
5. Saved in same folder as the WinISD.exe as WinISD.exe.manifest
It scales large enough to be usable now.
The text doesn't look real great, but compared to having to use a magnifying glass it is awesome.
(letting windows attempt to make it look "less blurry" only makes it worse)
EDIT: Worked well on WinISD, but on the other program (Family Tree Maker 2014) where the boxes didn't scale with the text it made things worse. I can live with it. Glad to have WinISD usable.