Are you fly sparging or batch sparging?
First thing to do is to, as accurately as possible, track your volumes. It is much easier to do when batch sparging than fly sparging. For batch sparging, measure your water input (total water) and pre-boil volume and the difference would be the amount of water left in the grain. Using this and your grain bill, you can calculate your grain absorption in fluid ounces per ounce of grain.
You seem to have a good lock on your boil off rate, so you are set there.
Next is to measure your post boil volume and volume to the fermenter. You will need to subtract the thermal expansion value from your post boil volume to correct it to room temperature (which I assume your volume in the fermenter will be). The difference between this corrected volume and fermenter volume will be your loss to trub and chiller.
Next thing to do is to look at your recipe which you just brewed. On the 'session' tab, enter in your measured values and the program will calculate your actual mash efficiency and brew house efficiency. You can use these figures to update your equipment profile along with the measured volumes of your losses. Your grain absorption can be updated under 'options' > 'advanced'
Now, if you fly sparge the values after the mash remain the same for calculation purposes. The grain absorption and any mash tun losses become somewhat dependent upon your sparging technique. Some people calculate and prepare the exact amount of water needed, in which case you can treat it as a batch sparge for purposes of the grain absorption calculation. If you instead prepare excess water and sparge until you reach your intended volume, the figure for grain absorption really doesn't matter too much, so you should be set with the default value.
If you find you are off in mash temperature, you can make an adjustment in the specific heat or the mash tun weight to tune this in. Reset the target temperature in your recipe to equal your actual measured temperature, make sure the equipment and grain temperatures reflect your measured values, and now you can edit the equipment profile within the recipe and adjust the mash tun weight or specific heat until the calculated strike temperature matches your actual value. Save this equipment profile and then click on the disk icon next to the equipment profile to save this new version. I usually add the date onto the equipment profile name so that I can tell if I have the latest version in the recipe.
You will need to update any other recipes already existing with your new equipment profile.
Now, the estimation of FG is always a questionable calculation. There are so many variables that contribute to the actual attenuation of the yeast such as: pitching rate, yeast health, fermentability of the wort, grist composition, fermenting temperature, and so forth. I use the estimated FG value as a guideline. If you really want to know the ultimate FG of the wort, you can perform a forced fermentation test and see where that takes you for FG.