The dead bees won't hurt anything. They are probably slow to clear things out because they aren't that strong right now. You can take off the super and set it aside, then dump the bees off the bottom board (or scrape them off) then move the super back. 2.5" of dead bees sounds like a lot to me. How many were left?

Mold it normal and should't hurt anything. Adding Honey B Healthy to the syrup will prevent the mold it becomes a problem.

-Tim

Phew, thanks for your help! I think what happened was that the package was submerged in water in transit. The dead bees were soaking wet at the post office, and 3 other packages there had the same problem, with dead bees stacked to the same level. We'd had a heavy rain, so maybe they were placed in an open mail canister. More than half of the bees were still alive, as well as the queen. When I called the supplier I was told that replacement, though free, would take up to 3 weeks and postage would be my responsibility. They said that the colony would replenish itself with no problem, and that I should be fine installing as is. Have I been had?

There will always be some dead bees on the bottom no matter how well they are shipped, though 2" sounds like a lot to me. If they PO actually did soak the bees it would explain thing, though if they were insured you probably could have made a claim (though they aren't all dead so it might be a tough case).

It sounds though like the supplier is right and they will likely do just fine though could take longer to build up. (hard to say without looking at them) The supplier was good even offering a replacemnt (some don't and just rely on insurance if it even applies). This year though I'm surprised they were even able to replace the order at all, let alone in 3 weeks. Many suppliers have been well behind schedule due to the rain and I have heard reports of both package bee and queen shipments outright canceled.

You should expect the number to drop some over the next several weeks after installation as old bees die, but when the first brood starts hatching they should start taking off.

-Tim

Things that the books don't tell you. Instead of banging the bees around trying to get them out of the crate, try this. remove the feeder and queen as usual and then turn the shipping crate on its side. put a deep hive body (empty) and hive cover over it and let them do their thing.
most of the dead ones will stay in the crate. Remember to remove crate in a day or two.
I may get some argument here but::: Soggy wet dead bees arre a sure sign of being overheated.

I concur on the soggy wet bees, and an insurance claim should have been made for overheating. Simply left in the truck for very long would do it.