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Do NOT put anything damp directly over the eggs. Direct contact with moisture will cause major problems! You're in the final stretch with these eggs so you should expect to see denting in the last 20 days or so before they hatch. You'll be surprised at how dented they will become in the last few days before hatching. Make sure you're giving them good ventilation during this time.

I wasn't clear on this when I started my first incubation but to get a day 49/50 hatch you needed to up your temps slowly over the last two days of the first week to reach your 5 week 88-89F temps, and then two days before your last week start to slowly drop your temps down for the final week of 85-86F. In other words, start cooling down your temps slowly about 48 hrs prior to your last week so that your entire final 7 days are at the 85-86F temps. Does that make sense? If you didn't do this, your incubation time may vary from the 49/50 hatch but that's no big deal.

p.s. Post some pics so we can see them!

A couple of those do look a little too dented. I don't have any experience with the substrate method of incubation since I've gone no-substrate both times. 1) Your incubator isn't saturated and is pulling moisture from your egg boxes and your egg boxes may not be humid enough. I'm not sure I know what your incubator set up is like. Do you have open containers of water to saturate the air inside the incubator? 2) Switch the cluster of badly dented eggs onto straight, damp vermiculite. I don't know how perlite works at all for chondro eggs. It may be too dry. Do you know how to set up an egg box with vermiculite? This should rehydrate them.