>>Rarely being able to find the queen anyway...

Was yours a drone layer?  Marking queens makes find the queens SO much easier.

>>..putting an excluder over the #2 box, a super over that and (former) brood box #3 on top.

What was your goal?  Why the excluder and a super?

>>For all I know that may be the case...

It's pertninent to identify the status quo fairly accurately before undertaking any steps.  It will save you considerable time and give predictable results.

>>instead of getting a queenless brood chamber to which I could add a queen, I now have boxes filled with bees with no mated queen.

You don't want to take any chances with laying workers.  New queen acceptance becomes a Russian roulette.

It's best to find the failing queen and dispatch her.  Just in case there are laying workers with a significant following, place the entire hive over a strong, queen-right hive.  The laying workers will be disposed of in short time.  

To introduce a new (valuable) queen, make up a nuc with 3-5 frames of emerging brood some covering bees.  Give this nuc about 24 hours for older workers to return to their original hives before introducing your queen.  Your acceptance will be almost 100%.  In fact, direct queen release works well.  I'll watch the queen walk out amongst the bees and watch for possible aggression.  If the workers inspect her and seem 'in awe' or surround her in admiration for a couple of minutes, I gently close up the nuc.

2 or 3 days later you can re-establish the old colony by either adding frames of bees or interchanging hive locations.

This is extra steps but your success rate will be close to a 100%.

Waldemar

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