After a lot of searching and testing, this is what I have come up with. There seems to be some confusion on how this works, and this setup has worked very well for us. Hopefully this will help someone avoid the amount of searching and reading I had to go through!
With your project loaded in the Sheet Set Manager (SSM):
Right-click on a sheet
Click “Manage Page Setups…”
In the Page Setup Manager, click “New…”
In the New Page Setup dialog, type: “42x30 PDF Horizontal” (This is what we use in the office so it shows up horizontal in Adobe)
Click OK to continue.
In Page Setup, the fields are as follows:
Page Setup: 42x30 PDF Horizontal
Plot Style Table: WhateverFileYouUse.ctb
Printer/Plotter: DWG to PDF.pc3
Shaded Viewport Options: n/a
Paper Size: ARCH E1-L (42.00 x 30.00 Inches)
Plot Options: “Plot with styles” & “Plot paperspace last” should be checked
Plot Area: Layout
Plot Scale: 1:1
Plot Offset: X: -0.5 & Y: 0.0 (This one you might have to play with. These settings worked for us)
When finished, click OK to continue.
The Page Setup Manager should show the new setup at the top of the list.
Click Close to continue.
You now need to select which files you want to plot within the SSM. If you want to print all files for one section, then simply right click on the section heading. For multiple files within the heading, hold down the “Ctrl” button on the keyboard and left-click to select which individual files you want to plot.
With the files selected, right-click on any of the selections…
Click “Publish using Page Setup Override”
Click “42x30 PDF Horizontal”
By default, the pages will be sent to your “My Documents” folder on your computer.
To change this, right-click on the main SSM heading, click Publish, and click Sheet Set Publish Options. In the top field (Default output location) you can direct where AutoCAD will place the files for that project.
Depending on your AutoCAD settings, the pages will be either in one PDF or individual PDFs. To check or change your settings, type “PUBLISHCOLLATE” in the Command Line. A setting of 0 will result in the PDFs printing as individual files. A setting of 1 will result in an output of one PDF file with all pages within.