Theres a lot of reasons for low hatch rate so a few more details will help.
Are the eggs shipped or bought local? (40-60% on shipped is not that low)
You are doing the right thing by checking the eggs to see when they failed and early fails can be a sign that your eggs are fertile and beginning to incubate before you place them in the incubator. As we don't know yet if these are shipped, local or how you handle the eggs before they are placed in the incubator its just a guess. I know in florida where its hot eggs have to go straight in the incubator as soon as they arrive and if the post is running late its going to be a bad hatch rate with lots of early fails.
even local pick up in warm weather can be a problem as 85-90 degrees seems to be high enough to start the process.
Do you have any diy skills as a 9 to 12vdc plug in transformer (the type that where the transformer is the plug) and a 40mm computer fan can be added to upgrade you to a forced air incubator (9vdc would be best so the fan runs slower and stirs the air rather than blasts the air but anything you have laying around should be ok). If you need assistance with adding a fan then im sure we can do a step by step photo guide that should work).
I guess the whole point of this post is that you may be doing nothing wrong. Even the best $500 incubators fail to hatch infertile, broken air cell, pre-incubated eggs, layer vitamin deficiency, etc etc. There are ways to up the odds but that's has to be fixed before incubation.
Oh forgot.
Another important measurement is the hatch day that any successful chicks hatched in the past. Were they early or late compared to dates other people surgest as that's a sign of weather your temps are correct.