A reaction to food could possibly be the case, although most do not get any reactions to applesauce (unless there is cinnamon in it). Try cutting out the apples and see how it goes. You can try it again in a small amount in a month or so. Also could be the diapers.
Use paper towels or wash cloths with water instead of wipes and change often. Try to change him at least once at night if he will be ok with his sleep.
As for the rash, have you tried the basics? When there is a diaper rash, you should first try a petroleum jelly based product, and if that doesn't help, then move to a zinc oxide based diaper rash cream (the highest percentage you can find). Also, let the boy rum around without a diaper on. To make this a little less scary for you, wait until your son poops, then don't put on a diaper. The fresh air usually helps. If you are having problems with a diaper rash that will not go away after 4-7 days, go to the doctor! If the previous mentioned methods do not work, you will need a prescription. My son never really got diaper rashes . . . as soon as he would get a little red, we would start the process and it would clear up withing a day or two. But, we just went to the doctor last week for one that lasted a week. The pediatrician said it was a fungal infection and gave us a prescription. The rash was gone in 2 days!
It sounds as though he is suffering, so I would get him to the doctor as soon as they can schedule it, and in the mean time, try the other methods.
Good luck!