New package of bees with queen issues

[Bakersdozen]

This isn't a question about actually raising queens.  It's more of a "what would you do?"  Here's my story.
I installed a package of Italians  Put queen cage with corks in place for 4 days.  On the 4th day, all looked well.  I pulled the cork out, watched her go down in between the frames.  No signs of balling.  Closed it up and came back 7 days later, yesterday, to check on her.  There was no signs of a queen but I did see some fanning by workers.  The only eggs or larvae I could find were 6 uncapped queen cells.  Bees were all over it and I couldn't see down in the cells.  Also had perspiration in my eyes.  The workers were taking the sugar water and back filling the 4 frames of drawn comb I had put in there.  Six frames were foundation and no comb. I thought I saw pollen being brought in about 2 times.  Not nearly enough if the situation were normal.  The bees demeanor was very gentle.  I closed up the hive and called my supplier regarding the queen.  He replaced the queen and I went back to install the new queen 24 hours later, today.
I looked in the colony before leaving the new queen.  3 queen cells were capped.  I was able to look into the 3 uncapped queen cells and saw about 3 day old larvae.  Out of curiosity I laid the new queen cage on top of the bars to see the reaction she would get.  They were a little excited, but not agitated.  The general demeanor was still gentle.
I left the new queen cage with corks in place.
Here are my questions:
1. Did they allow the original packed queen to lay a few eggs before killing her?
2.  What are the chances of those eggs making good queens? 
3.  To keep the hormone levels normal, should I have cut out the queen cells?
4.  This colony is all alone and in another town.  Should I make a split, take it to this yard, and put a frame with queen cells in with the split.
5.  What are the chances of the workers accepting her with 6 queen cells present?

Thanks for letting me bend your ear!  Opinions welcomed!

[iddee]

First, I would have told the supplier what happened, but to wait a week to see what happened. Since you now have the new queen in hand, I would remove the queen cells and let the bees remove the candy and release the queen. I have never direct released a mated queen.

[Some Day]

I think it takes Twenty to Tango if you have a new virgin queen. Do you have any mature drones in the area to mate with the virgin queen if you let her hatch?

Since you already have a replacement queen I would cut out the queen cells and see if they like your new mated queen.

Here locally we do not have an abundance of drones yet, so a new virgin queen would not be mated very well.  I don't know about your area.

[Bakersdozen]

Thanks for the replies.
Iddee, I called him before I ever drove off from the yard.  I guess I was expected him to offer me some insight on what was going.  He just wanted to make sure I had a viable queen asap.
Some Day,  I have drone cells in my other colonies.  This colony is located in a different town.  The only drones I know for sure are the ones that were in the packages of bees that I installed.  I  keep thinking the presence of capped and uncapped queen cells are going to make the pheromone levels crazy and the workers will not accept the new caged queen.

[iddee]

I would set up a nuc with the new queen and wait about 3 weeks for one of the cells to emerge and begin laying

[Lburou]

I would set up a nuc with the new queen and wait about 3 weeks for one of the cells to emerge and begin laying

That is an excellent plan B!

[Bakersdozen]

Following up on the queen issues, this is what happened.
One day prior to the emergence of the first of the queen cells, I pulled some frames of brood and nurse bees out of a thriving colony in my back yard.   I took those frames, in a nuc box, to the yard with the new package.  I put the frames with the queen cells and their nurse bees in the nuc box.  I reduced the entrance and put a jar of 1:1 sugar syrup on top.

The new replacement queen, still in queen cage, was still in with the package of bees.  I pulled the cork and let them slow release her.
Today I went back to check on the progress of both colonies.  The package of bees had released the replacement queen.  There were lots of eggs.  Pollen was being brought in and wax was being drawn.  They were quite docile.

The nuc, with the 6 queen cells, was not as mellow, but not stinging.   Understandable, I think.  They have experienced a lot in the last week.  Just like a text book, I could tell the queen cell that hatched first.  She then went around to the other 5 queen cells and took a big hunk out of the sides.  I didn't see her but pollen was being brought in.
I refilled the 1:1 sugar syrup on both colonies and called it good.

A Master Beekeeper told me something that I think could be true.  She thought that the bees allowed the queen, the original queen that came with the package of bees, an opportunity to lay a few eggs.  They planned to supersede her and then they did her in.   She said that she had seen it several times before.

[iddee]

I have heard it happens as high as 60% of the time with mass produced queens shipped with packages.

[Bakersdozen]

I have heard it happens as high as 60% of the time with mass produced queens shipped with packages.

Good to know.  This was my first experience (that I am aware of) with this behavior.  But I am just a hobby beekeeper.

[tecumseh]

a snip..
'He just wanted to make sure I had a viable queen asap'

Well first off with that attitude you need to keep that queen supplier.   Sadly I hear too many stories of queen producers who do not have the same attitude towards making certain their customers are happy with their purchase. 

The Nebraska Test which took place decades ago ( ie I do not even know if I still have a copy of that experiment) which indirectly pointed the finger at nosema a. as the culprit and set about a florist in the use of fumidil by queen producers. This was a blind experiment conducted in Nebraska (thus the name) that bought packages from half a dozen queen and package producers and then monitored how many failed outright and how many queens were quickly superseded.  There was (as far as I can recall) great variation in the failure rate with the numbers of some well respected queen rearing folks going as high as 100%. The operation just down the road in Navasota had a failure rate of 0%, with the study pretty much putting him (Roy Weaver) on the map as the king queen rearer of his day. 

Now we have nosema c. and as far as I know no real cure for the problem but the history of both nosema a. and c. suggest both clear up on a good honey flow. Which makes identifying the culprit a bit random.