I've only hatched a few leopard geckos last season, but here are my thoughts.
1) I put around 5 pinholes in my containers. But that was only because I kept water in the bottom of the incubator, limited ventilation in the incubator, and made multiple test runs for the length of the incubation. I would recommend making a few cups just experimenting without eggs and see what works best.
2) If they get mold or fungus you can use athlete's foot powder. I don't think that they are always dead because I've seen terrible eggs end up hatching. And also, it doesn't hurt to try to treat the mold in hopes that it might hatch. "Incubate until there's no debate"
3) Most of the time first-time females' first clutch is infertile. You will likely get multiple clutches so you should have multiple chances. But, having only paired them one time lowers the chances of successful fertilization. Last year, I planned on pairing every 2 weeks until the first clutch.
4) It could happen but it's not likely. If you're worried about it you can rinse it off and soak it in water (if you have a way of easily removing the water once it's done).
Hovabators are infamous for being the wrong temperature. If you decide to use it you should at least cross-check the temperatures with one or two thermometers. You can also build an incubator very cheaply that will likely be more reliable. Last season I used a Farm Incubators Still Air Incubator model 2100 (which was given to me) and it worked great. I also liked that it had a window, because otherwise I would be opening the incubator a few times a day to check on the eggs. Which might have resulted in temperature inconsistencies.
I think a 1:1 vermiculite:water ratio is perfect. That's what I used, I did need to add a little bit of water later in the season, but I used a lot of ventilation.
Using a fan helps remove temperature inconsistencies inside of the incubator but it doesn't help temperature fluctuations. The best thing to do would be get another incubator, but if that's not possible you can make this one work.
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