Hey Mike,
I have no real answer on the saddle bags. Do you have a trunk already? That's the common solution for getting more storage space, good and inexpensive. Saddlebags you need to physically try on if they really fit; they should be available at larger motorcycle dealerships that sell sport bikes.
As to the vibration I think you have a rusty clutch bell that causes this vibration, once engaged it is not existing.
The "red neck way" you can hold the front brake and give it slight throttle (engine running) and let the clutch shave the rust off, which will happen after a while (e.g 10-20 seconds). You can also do this in two, three, four steps with cooling time between not to overheat the clutch surfaces hopelessly.
Professionally you would need to take the clutch assembly off and with sand paper remove all rust and any uncontrolled friction materials that may have built up. Clutch pads and clutch inner housing surface need to be 100% smooth.
But if the scooter sits for a while in a damp environment you will have the same symptoms again very quickly. Regularly using the scooter is preventing this.
Addendum: Red-neck version No1 does work fast, but will abuse/use up your clutch pad assembly quicker over time. However, it is not an expensive item if time comes to replace it.
WW