Well, It looks like when you read tonel files with your changes there are some "invisible" characters left over in the stream.
I think that first you should be able to reproduce the issue locally without bootstrapping by trying to import a tonel file in an image with your changes.
Just take any of the files inside Pharo's src/ directory and try:
reader := TonelReader on: stream fileName: '...'.
reader loadDefinitions.
Once with the monticello definitions you can try to compile them or check if the source code in the methods have something strange...
If that fails, come back and we can do a skype trying to show you how to bootstrap :)
Guille