Okay, I am getting closer on build 2. My question is, " Do I place the bridge at the 25" mark or can I place it back on the box?" If I place it further back that will change the scale and the frets will not be right. Is that correct?
For a given scale length, your nut and bridge absolutely must be separated by that distance (leaving a little wiggle room on the bridge end for intonation adjustment) or your fret spacing for that desired scale length will be completely wrong. If you already have the neck or fretboard fretted, the only way to move the bridge is to change how the neck is placed relative to the box, moving the box up the neck would allow the bridge to land nearer to the back end of the box.
If you haven't yet fretted things you could use a longer scale length to allow the bridge to land further back, just realize it increases your fret spacing and may also raise the string tension. Hope this helps, good luck!