Well, I bit the bullet last night and tore everything back apart again.  It turns out that I think my leak was just coming from the rear of the oil pan gasket so I hope with a little scraping and a careful RTV silicone job that'll be taken care of.

I think my vibration problem is coming from the rear of the coupler that connects the main input shaft of the transmission to the engine. The splines on the main input shaft look like they're pretty worn down and the hole that the set screw (or bolt) is supposed to go into looks over sized.  I remember it vibrating before I tore into it last year so it's probably something that's been a problem for a while.  Anyway,  I think I'm just going to live with it for now as the tractor won't be used much and I'm guessing you have to remove the transmission top cover to change it. 

Any suggestions as to something I can do or put in there on the splines for now to maybe reduce the vibration?