A couple of things- if it's started vibrating... you might have had a rodent or bug intrusion. That would create a 'dead zone' where air has to rush around (probably in the 3" section). The exhaust motor would work harder to overcome this, and that would shift things.
Your house could also have settled, and the wood could also have swelled slightly with moisture. As the winter dries out, everything goes back to normal and the pipe stops rubbing.
Vibration can be carried up the pipe as well, so you'll need to lay a hand on it (or a cell phone, say) and 'listen' to the pipe. Maybe you can track down where it's pinching at and causing the noise.
You could also download a spectrum analyzer app to see what's the main frequencies of vibration. Might be fun to see.
As for putting in a fernco, the answer I remember was 'no'. Basis being ferncos can not be used on pressurized systems, ever. And that won't necessarily fix the issue, either, depending on where the problematic sound is coming from. The manual should state the venting requirements of the furnace. And a quick call to your local code office should give you an idea too.
Here was a quick google-