The fact that it's worse when it's cold makes me think tires. I've had a lot of tire issues over the years because I used to roll almost exclusively on used tires off of cars that were headed for the junk yard. When I still lived with my parents, I had access to all of my father's heavy equipment and we would scrap old cars regularly. Any tires that had decent tread on them would end up on one of our vehicles at some point (back then almost everything had pretty standard 14-15" sizes that were interchangeable between many different brands). This tire swapping often caused the belts to shift because of varying rotation/alignment on different cars along with them being old and starting to dry rot. The vibration from a shifted belt is worse when you first start driving, and the worst when it is very cold outside. When you get the tires warmed up the pliability of the rubber increases so imperfections get smoothed out and it feels better when you're rolling. It's very similar to using bias ply trailer tires which get flat spots in them when you leave them sit. Drive until they're warmed up and the vibration goes away when the flat spots disappear. The way I would check for this is to jack up each tire and (with gloved hands at first in case any steel belts are exposed) check for imperfections around the whole tire. You'll feel a pronounced bump if the tire is out of round from shifted belts.
If you find this condition, get new tires IMMEDIATELY. The imperfection will cause the tread to wear through in very few miles, then the belts, then your tire pops. I have had this happen on new tires too, which is actually the only time I've had a tire blow out amazingly, so new(er) tires don't exclude this as a problem.
Something else of note in your posts is that you said the PTU was recently serviced, which means that your driveshaft was disconnected. If this wasn't indexed properly during reassembly, it could be causing your vibration, because even while in neutral rolling down the road, the front axle half shafts, PTU and driveshaft are all still spinning. Other than wheels/hubs/brakes/tires, the PTU, half shafts and driveshaft are the only other things that could cause the vibration since it happens independent of the engine and transaxle being engaged.
