pglover19,
Measure from the sill up to the bottom of the top trim (the trim the runs between your transom and the entry door unit. Hopefully that measurement should be somewhere around 80". If the measurement is 79.25 or 79.5 look at removing the trim and moving it up so you get 80"........just make sure the trim does not stick up past the base of the transom creating a trap for water.
Another thing, your "buildout" looks like it's only around 1.5", how far out does that handle stick past the existing mull? If the buildout extends 1.5" that will make the storm door recess back to about .5" from the existing trim....might have a handle issue.
The 4000 door since it's a fullview can not be cut down! The door will fall apart since the whole integrity of the door comes from the angle slugs in the corners. The bottom expander is needed to compensate for your opening being out of square and to keep daylight out. Removing it will only get you about .5" but it defeats the purpose of your door.
Another thingy, the insulating glass is a waste of money! It will put to much strain on your hinge z-bar (frame) and will cause your door to fail long before using normal glass. While the glass is insulated, the rest of your frame is metal and will transfer heat. Your entry door should keep out the cold just fine without needing a storm door or at least a storm door with insulating glass.