I think you are a bit confused as to what constitutes a shook swarm. I got the following by typing in 'description of a shook swarm' on google and is what I understand to be a shook swarm.
Background
It is now a generally accepted fact that regular changing of brood frames (and combs) helps to inhibit brood diseases, such as Nosema & EFB. Colonies treated to wholesale frame changeout often become the most productive in the colony.
Until recently, frame replacement has been advocated on the basis of one third of the frames every year - ie. a full replacement every three years. However a recent technique, called "Shook Swarm", aims to replace all brood frames in a single operation, thus removing all potentially diseased equipment at a stroke and minimising disease transfer (a perceived disadvantage of the "Bailey Comb Change", which is the alternative method of complete brood frame replacement).
Timing and Suitability
This technique should only be carried out on strong colonies capable of enduring the stress it undoubtedly creates. It should be carried out as early as possible in the season, but certainly not later than July. Ideally, a good nectar flow should have started, but feeding will undoubtedly be needed to help the bees rapidly draw out the new comb.
The Method
You will need the following equipment :-
A clean brood chamber, containing new frames of foundation
A queen excluder, crown board and floor ( all clean).
Contact feeder with heavy syrup.
Move the existing hive to one side and assemble the new hive in its place, with the queen excluder between the floor and the brood box.
Take out the centre 4 frames from the new hive and place to one side.
Find and catch the queen in the old hive and confine her temporarily to a queen cage or other suitable receptacle.
You must now transfer the bees from the old hive to the new one. This is done by taking each frame in turn and shaking it into the space left by the 4 missing frames in the centre of the new hive. Any reluctant bees can be gently brushed off. Once all the old frames have been cleared of bees, shake or brush all the bees remaining in the brood box into the new hive.
Remove the queen from the container and place her in the centre of the new hive.
Carefully replace the 4 missing new frames in the new hive.
Fit the crown board
Feed with heavy sugar syrup - ideally using a contact feeder on the crown board
Apart from regular feeding, do not disturb for about one week, at which point, brood should be present. Once there is brood on the comb, the queen excluder can be removed. Continue to feed, unless there is a good nectar flow, until all combs are drawn out.
Possible Disadvantages of Shook Swarm Technique
If queen is lost, or damaged in the process, then, because there are is no brood present, the colony will be lost. The queen excluder must initially be used below the brood box to prevent the queen absconding.
References :- Fact Sheet 16, National Bee Unit, South West Region by Richard Ball
Yes you have seperated the Queen from the rest of the brood but the bees are still all in the same set of boxes. You have not done a shook swarm. As to your question about getting the queen to move up into another box, what I do is take half the brood and store and stack it directly ontop of the remaining brood and stores in the centre of the brood box, filling with foundation or drawn comb on the outside, allowing the bees to expand on both levels. If the colony is strong enough to do this then once both brood boxes are fairly well drawn and have brood then its easy to put a queen excluder between the two boxes wait 4 days and check each box for eggs. The box with no eggs has no queen. Place to the side and shake in bees if nessesary then add a bought in queen. If you are splitting one hive why go through the hassle of trying to rear a queen when you can get one for £30 and she will begin to lay almost as soon as they let her out of the cage.
Honestly, I have done some silly things with bees too and it sounds to me that what you have done is mix and match bits of several different operations into your manipulation.
What I have found is that to make sustainable increase, the colonies from which you are taking the key elements of brood and stores are strong enough to bear the strain of the sacrafice. As to the fact that they swarmed, I honestly dont think you should believe the bees swarmed because of you having a rumage round within 24 hrs. Bees do not want to leave brood and stores which have taken a massive amount of time and effort to accumulate and head out into the unknown with nothing. I have been making the most of the weather and have been in and out of most of my hives almost all week making up nucs and boosting slow colonies.