2005 tacoma vibration/ shudder

I'm experiencing this right now. A wavy bump around 28-31mph, and another quicker sharper vibration from 35-38mph. Truck is at the dealer right now and they said it appears internal to the transmission and it'll be $5,300 or so for a replacement. That and a leaky power steering boot and shot rear struts leads to a potential bill of over $7,000. At that point, I'd might as well drive the truck into a hedge and start new.

So I'm curious if it is something like the mounts.

For the record, it did this something like 18 months ago for a few weeks. I went in and they flashed the ECU and said if it continues that the tranny will need replacing. It continued for maybe 3-4 weeks afterwards, then was fine for something like 17 months. So could that be a mount where it went bad, then something happened where it held ok for those 17 months and then slipped and is going silly again? I'm an IT guy, so the troubleshooting part of my brain tells me that it really doesn't make sense if something is messed up internal to the tranny....then it fixes itself for 17 months and then goes bad the exact same way again.

Edit: 2009 TRD OR double-cab with 111k miles. Always followed strict factory maintenance scheduled service.