Just starting to shake after things had been working fine all this time?
Strange that it goes away when you push the clutch. And it's a real shaking, not a simple vibration?
Very strange.
I'm not sure yet. Haven't run into something like that. Maybe someone else has some insight.
When the clutch pedal is depressed, the flywheel and clutch cover are still spinning with the engine. Only the clutch disc and transmission input section stop (or come close to stopping) their spinning.
Maybe the disc is deteriorating? Hate to think it's something in the transmission. Did you use the specific gear lube that's required for the 3550? Checked it's level and condition lately?
Just for our information, what else has been done to the engine? Is it a stock 289/302, or is it something else? (edit: nevermind. I see you have it showing as a 302)
Good luck.
Paul