The tiny bugs sound like mites. Remember that most mites are not parasitic species. They feed on detritus in terrarium soil. I doubt anyone has a terrarium that is free of them. So those I wouldn't worry about. In a well planted (live plants) terrarium, with decent micro fauna (spring tails, etc), you almost never have to change the terrarium soil. For substrate that is just there as substrate, it really depends on depth and the number of animals that are dropping faeces into it, but a safe routine would be to replace at most every 1-2 months.

It sounds to me like your tree frog is suffering from a bacterial septicemic infection, brought on by a stress factor that I can only guess at since you haven't given us any info on temperature, humidity or terrarium conditions. At this point the frog's only hope is a trip to the vet. I don't believe you can save him on your own.