"Any suggestions on what to do to improve the humidity or if it is even a problem? Most of the eggs look good."
Depends on your setup; incubating medium, tub/container/lid, the type & design of the incubator, etc.
Most of the inexpensive indoor/outdoor thermometers that also measure humidity are accurate enough. The lil' stick-on humidity strips & dials sold in pet shops aren't. I would place an indoor/outdoor therm. in the tub(s) and make sure it's at least 80%.
As long as the eggs don't collapse much further than what you've described they should be fine. If you see them continuosly collapsing you'll need to add a tad more water to the substrate. I usually use a spray bottle with warm water, set to a fine mist, if needed. If there's room in the tub(s) to set a small container of water in, go that route.
The eggs in the following photo were in pretty bad shape, as you can see, but the majority of them still hatched since I stopped the loss of humidity.

"I had a very hard time getting one of the boxes of eggs to regulate at 88-90 today. For several hours (5-6) they were under temp and in the 85-87 range. I think I finally have it worked out. Do you think that the cooler temps during that time frame is a killer?"
They should be OK as long as you eliminate or reduce the drop so it's not a contiuous thing or lasts longer than that time frame. Now you see the importance of setting up & running the incubator about a week before it's needed so those kinks can be worked out without endangering the eggs. If we'd all be honest, most people, if not all, that have incubated eggs have found their self in your shoes. Been there, done that, myself. 
If you're still having trouble getting fairly even temps all-throughout your incubator, post your setup info and we'll see what's the easiest, best, route in your case. Could need to add a small heat source in a specific location, heat deflector(s), installing a small computer fan in the right location, etc...
Hang in there!
HH


-----
Due to political correctness run amuck,
this ol' hillbilly is now referred to as an:
Appalachian American

www.natures-signature.com