I have no idea what you meant by that, but it sounds/looks rude.
I'm assuming because these are the hotkeys ISboxer uses, and that if there's a way to free them up, I'll be able to use them for my straight key broadcast/straight key broadcast+click functions the way I want to.
So, that leads me to ask how one would go about making the Shift modifier available for usage?

This is not why they are disabled in the wizard at all. ISBoxer does not use Shift, Ctrl, or Alt as Hotkeys and neither should you (which is the reason they are disabled for Straight Key Broadcast) because you would unintentionally break things in order to get what you may believe is a shortcut.
By step one I assume you're saying mapped key wizard >Combat >Straight Key Broadcast, right?
No, he didn't mention the wizard at all actually.
The problem is that you started with the wizard and instead of doing what you were supposed to do -- hold Shift while you press 4 because that's how the Hotkey Shift+4 works -- you put in just 4; and then after the wizard you came out and changed the Hotkey (what you press) to Shift+4, but did not change what ISBoxer sends to the game, which is still 4.. You could have gotten exactly your current result by selecting "Key Re-Map" during the Mapped KEy Wizard instead of "Straight Key Broadcast", and tell it to press 4 when you press Shift+4 -- this doesn't sound like what you want.
Here is what he was saying by "you need to go into Step 1 and change the Key Combination that's being sent":
In the top left pane under Key Maps, select Combat. Then in the bottom left pane you have a Mapped Key that's "4 (Hotkey: Shift+4)". So expand the mapped key called 4, so under it you see "Advanced, Steps, 1" and click on the 1 under Steps. Now to the right you see "4 -> Shaddafackap-Moon Guard". If you want it to send Shift+4, select this Action and adjust its Key Combination to include Shift.