Jerry you are doing real good.
Incubating eggs is so unpredictable with so many variables anything can happen.
So far though your percentage is great.
You were right to take those other chicks out, thats alot of babies in the bator running aroun and they probably were getting overheated.
Plus like I said they get bored and start pecking at the newer hatchlings.
The ones that were dead in the shell could have just quit. It may have had nothing to do with you opening the bator which you had no choice in anyway since it needed to be done, but sometimes you just get quitters and you never know why.
They may have quit a couple-few days before the hatch even.
Finding fully formed chicks dead in the shell is actually quite common, even when its under a broody hen.
I hope the rest goes well for you. Its tough sometimes to know when to call the hatch.
I should not tell you this

but once when I fininshed a hatch and there were some unhatched eggs I was on the fence about tossing the eggs.
I kept wondering whether I was making the right decision but they were late hatching so I cracked the eggs to prove it to myself and 4 of them were alive but the egg shells were like rocks and they couldn't peck out.
The first one I cracked I was so nervous because I didn't know what I would end up finding but as soon as I broke the top of the shell the chick peeped really loud and pushed its head up out of the egg.
I helped him out and he was fine and healthy.
I got the nerve up to do the rest of them and had 4 other chicks do the same thing and I almost threw them away.
Some had a liquid start to seep out the cracks and I did not go any further since it was obvious there was no chick.
I think it was day 23 and the others started hatching on day 19 so this had been going on for 5 days so I think it made me feel like it was later than it was and they weren't going to hatch.
Those shells were so hard I actually had trouble breaking them so I really highly doubt they would ever have gotten out by themselves.
I still have all those chickens running around my yard.
Candling is much easier to tell after the first week but then by the time its the second week the only thing you can see is dark shadows, it takes some practice to know what you are looking for.
I don't use those candlers. I went to walmart and bought a small powerful flashlight, the kind you would keep in your glove compartment.
They are the metal ones that come in different colors and cost like ten bucks.
After the chick has been in the bator for 7-10 days you can take the egg out and shine the light straight down on the egg in a very dark room.
They usually recommend you do it from the bottom but I can never see anything that way.
Just don't turn the egg upside down or you will tear the air sac and break the veining.
Keep it upright just like when you took it out of the bator.
You can see something that looks kind of like a chicken-dinosaur swimming around in the egg.
If you see nothing at all and you are sure there is nothing you can chuck the eggs or leave them until the next time you candle. I usually leave them because I want to make sure.
Some eggs are so pourous that you can see right through them and they are clear for sure and those I toss.
If you ever see a very bright red ring going around it but no chick then its a bacteria ring and you need to toss that egg right away.
If it explodes in the bator it will infect everything.
Don't confuse this ring with the regular dark ring that you will see at the top of the egg where the air sac is.
This red ring will be clearly red, not the dark ring where the air sac is, plus the egg is usually clear so its easy to see.
Also, you can see red veins all through the egg if you have fertile eggs.
Thats the easiest and the earliest way to see if they are fertile.
If you candle early and see veins you can put them back for a few days and then check them to see if you can see the baby swimming around.
Its actually pretty cool, if you shine the light the baby chick starts swimming around the egg, the light disturbs them and makes them move.
You shouldn't candle too often though, you won't be able to see much after the second week anyway, just a dark shadow but the egg will have some more weight to it.
You will be a pro at all of this by the time you are done.