Woke up to hear the dang tick.

[Get N Dirty]

Personally, I would get a second opinion on it. If it quiets down after engine warms it's likely the manifold which is a very common issue and easy fix. I know you say you trust the shop, but it doesn't mean they are right. If you have a different dealer nearby or within an hour or two drive, take it to them if it's under warranty still. Shop may just be looking for a nice repair bill. Way too often the "hemi tick" is mistaken for lifters when it's just the manifold.

Really could be a simple problem and blown out of proportion by this shop

They took pics of the manifolds and took off the heat shields, its not the manifolds. Yes I wish it was the manifolds. This owner had literally bailed me out before when I arrived near closing time with a problem on a vehicle and had a technician stay after hours to get me and my wife and kids back on the road. The owner often time is present, will walk you back in the shop and show you the problems. He often times is the guy who ends up driving you home if you need a ride. So yah I TRUST him. My truck engine is in pieces right now so kind of hard to drive it hours to another shop to have someone look at it. It cost me money for them to open it up to verify what the problem is. The Truck is NOT under warranty.