First, nothing that you did was wrong. It is just a longer way to get a QT tank in place. Generally the necessity of a hospital tank is an unexpected need to treat for disease.
Since you plan on using this as a permanent setup, you have multiple options at this point.
1. By all means, remove the shrimp. They cycle has started, and as pointed out by Nolofinwe, it has served its purpose.
2. The Emperor pads have already started to seed with the bacteria from the QT tank. Let them run their course.
3. If you want to get the ammonia level down faster, do a 50% to 75% water change using water from your main tank to replace it. Removal of the shrimp and the water change should help that along.
4. Put anything in the tank (PVC pipe, etc) that you plan on using if you haven't already done so. Primary bacteria cultures exist more on the solid parts of the tank than in the water. This will get the bacteria in place.
5. Put some sand from your established tank in. Since you want to make this permanent, consider putting in 1/2 to one inch of substrate (all of this does not need to come from your established tank). Fish seem happier with a substrate, and reducing stress is one of the keys here.
Since you do plan on making this permanent, let the balance of the cycle run its course. At least when the cycle completes, you will have a good comfort level that the tank can handle inhabitants. Besides, effectively you are setting up a "new" tank since it is permanent. The only bad thing that happened here is it was fed a lot more than it needed to be up front, so it may extend the cycle.
The first time that I had to setup a hospital tank (back in the 70s when I had shoulder length hair, unlike now when I'm glad for what I have left
) I had the same concerns, and not letting a hospital tank cycle defied all logic. Even a marine biologist assuring me that it wasn't a problem didn't help.
In my case, my QT tank has become a nano reef because my main tank is fully stocked and all of the fish in it have been there for long enough and get along well enough that I am very secure that they will be there for many years. As a result, I don't expect to be buying anymore fish for quite a long time. I hope you can tell me the same thing down the road.