1. Is okay to remove portions of substrate to re-wet them during the weekly touch up cleanings? I've noticed that my Eco earth is starting to dry out a bit and my humidity isn't staying as constant as it used to be even with misting.

Don't remove them, I honestly mist like amazonian rain. I don't have it set to pure mist, more like mist/slight rain. If you take a piece with poop out, just dump it, and rewet the rest.

2. What is the safest way to locate a buried Pac? I really freaked mine out while looking for poop the other day when my scooper bumped his/her face.

Hand digging, that's what I do. You shouldn't need to locate them, they will surface when hungry and if they stay down for a long time and you need to locate them, use your hands carefully.

3. If stressed, is it better to forgo a feeding when hiding out than to try and feed? I assume the reason Masterchief hasn't come out for two days is the event in number 2 really bugged him.

Mine is stressed right now because I moved her to a bigger enclosure, it really depends on the frog, I've offerd her food, she has declined, when she is burrowed I can't dig her up, my male on the otherhand, I dig up nightly to feed him, he doesn't care. Most frogs tend to be grumpy when unburrowed though.
Mine has now missed a feeding, and since she only gets fed twice a week, she missed out on one. It's better then reoffering food again and again and stressing your frog out.

4. Is it okay to turn on my bright red lamp during feeding so that I can actually see what is going on? The nighttime blue lamps are so dim that I practically need night vision goggles to tong feed.

I know what you mean, I use my cellphone flash light on the top of the enclosure. It should be okay to turn your infrared light (infrared doesn't bother frogs!) or another light on. Remember, the enviroment needs to be darker then normal, that doesn't mean you can't use a dim light.