I was able to get my system to work as follows:
1) Set the TV to use option 1 for inputs: " Method 1: Select this method if there is only one source input button on the remote, and each time the button is pushed the next input label is cycled to in a set order."
2) Setup your input list as follows:
3) Choose "InputNext" as the button that scrolls between inputs.
4) Since the first time you press the "InputNext" button, it only brings up the menu and you have to press select to actually select an input, we need to add a couple extra button presses. For each activity that uses your TV, add the following extra button presses at the end of starting the activity:
TV - Send "InputNext"
TV - Send "Select"
5) Since there is no direct input, the help button will not allow easy fixes when the inputs don't change correctly. As a "fix" I added the "InputNext" and "Select" button to my extra buttons for each activity so I can manually fix things for those occasions where an IR command is missed/skipped.
This was able to take me from fuming angry that there were no direct inputs to at least be able to tolerate it. This isn't a perfect solution, but it is definitely better than chucking my $75 Harmony remote. I hope this helps everyone!