Issue resolved.

So after I tightened the negative battery cable to the battery post, the vibration seemed to be less, gone at times but present at others. I took the runner back to Toyota, had the service manager come for a ride and again, at times preset and other times not. Like the vehicle was struggling, and then all of a sudden fine. I felt like he was down playing the vibration, trying to tell me it was because it is cold outside (-7 Celcius or 16 Fahrenheit). Not really all that cold at all, especially as the engine temperature was 1/4 between cold and hot, so the engine was warmed up. Then the tech tells me he really doesn't feel anything most of the time. I discuss the issue with him further on the way back to the dealer and he decides to have it booked back in.

The vehicle goes back in a week later, they scan the vehicle, run diagnostics and I get a call. They think it is one of the injectors. Now an injector, coil and something else is on order.

Vehicle went back in today, the injector, coil and whatever else was changed in cylinder #1.