Welcome to the GF family, I'm sure as you work out your process you will find it even better!
1) My Mash water calc would call for 6.94g, so considerably more and that alone will answer your dough in issue. I do not think I've altered the GF calc for Mash - I do on the sparge- based on a few factors (time, expected loss due to amount of hops, my boil off rate, lauter ability).
I came up with sprage, for a 90 min boil, of 2.44g, so my total water is still higher than yours (due to my adjustments) at 9.4g v 8.9g. Ha, there is that "missing" .5 gal!
2) Temp fluctuation, that's a bit odd, especially since you lowered your hysteresis to 1F. Did you have the lower button on mash (this will run the heater at 600w not 1500w and better control).
3) Lots of reasons there, but most common is grain crush. Was this from your mill, or store? We tend to crush finer than store, so this could be likely culprit.
4) Normal & Mash setting- ramping up to mash temp. Will use 1500w and stop when reaches your mash temp (btw, I use a +10-12F degree strike temp, just like the old cooler MLT days).
4a) Mash (bottom) & Boil (on controller)- not used. Boil on controller will override the mash setting on bottom and use the 1500w element.
Note, I am now hitting all my volumes and within a point or so of my OG. I just have it dialed in now, now your turn to dial yours in! Cheers!