I have yet to utilize the TOO mode for JDAMs but the one thing that I have gleaned from the forums lately is, the waypoint needs to be placed very accurately on the target with a 0 elevation in the ME so that it will be the correct target elevation in the a/c mission computer.
For the Pre-Planned release mode, I don't go through all of the steps you list there. I don't ever mess with selecting the stations or quantity. I also don't mess with selecting the terminal parameters. I just select the Mission up on the top, then TGT UFC over on the right. I then always enter Elevation (in Feet) first. I then go back to TGT UFC and then hit POS and start with LAT. There are 6 digets, preceded by either a N or S, (depending on the hemisphere) for DD (degrees), MM (minutes), SS (seconds), and hit ENTER, then 2 more numbers for the tenths of seconds and hit ENTER again. You should then see N DD,MM,SS.SS, E DD,MM,SS.SS Elevation underneath when you're done. Once the Elevation, Latitude and Longitude have been entered for the first target, I select the next Mission box up on the top and start over.
Once all of the targets have been entered, it is just a matter of bringing up the stores page, selecting JDAM, then JDAM Display and choosing one of the mission boxes. This assigns that target to the first JDAM to drop. I am pretty sure you can select which store comes off first but I have never done that. After selecting the mission box, I see a count down timer and an indication of where the target is on the HUD. I also see the target displayed on my HSI with a max/min range ring around it. You can enter data for many more targets than you have JDAMs for, which allows you to select whichever one you want to hit once you get there.