First step to creating tone changes is adding an event in EoF, give it a unique identifier.
Afterwards, under the tones section of Rocksmith DLC Builder, create a tone with matching names as your identifier.
For example, I have a song with a custom bass tone. Each song has a default tone, let's say I named it "bass_base". Under tones, I should have another tone named "bass_base".
Real Tone Cable will always have a delay, don't think you can do anything about it. I also use an audio interface myself with RSMods installed using the "Direct Connect" option instead of Microphone.
Import song in EOF, add silence
Notate your songs in Guitar Pro 8
Embed Audio Track (with added silence) in GP then set time offsets and signatures
Export to GP5 file format
Import to EOF
Save as Rocksmith XML
You can ((almost)) do everything in GP, only treating EOF as a converter.
I finished creating a CDLC
Issue is.... How do I create chord/arps and strums with GP?
Sure, notating HOPOs and slides with GP then importing it in EOF can be done, but not chords.
How do I achieve this with GP? I'm trying to avoid using EOF, it's by far the slowest and annoying part of the process.