There is a piece missing from your script: Page Setup/Print Setup
You need to test your layout with various Print/Page setup settings to find one where the entire area of the layout you want to print is included, then script that Page/Print Setup into the routine so the PDF is output/printed at that setting.
A very rough guess from what you showed is to start with a setting in 65% reduction range then fine tune it from there.
Save as PDF does not adjust layout content for you any more than regular Print commands in a script. You must take charge of that yourself.
I wouldnt have thought to use Print Setup if i werent actually printing the document.
I added the step, setup the page in Portrait Mode, set it to standard 8.5" x 11" and there appears to be no change. I don't see any other settings that will allow me to change the page to fit into the printable area.
I just find it odd that it's always the first page only
Looks like i've gotten it set correctly.
I didn't read all of the dialogues and found the options button on the specify options checkbox. On the Initial view tab i set the magnification to 75% and that appears to encompass the whole document.