Now that your machine is level, you will need to re-surface the spoilboard to make it truly flat before proceeding any further.
Zeroing from the spoilboard is not anything special (you may be overthinking this). No, you don't enter any negative numbers. Yes, the software compensates for the material thickness automatically, so no worries there. Just be sure you change the z-zero location (from the top surface to the bottom) via the Material Setup and recalculate the toolpaths before running your project.
No worries about the chips either - I use downcut end mills for cutouts most of the time (which tends to pack chips in the grooves). Chips remaining in the groove are no match for the router (in my case, the spindle). It doesn't care they are there and the router won't jam. BTW, using a downcut bit and allowing chips to remain in the grooves helps hold vacuum better anyway.
You don't need to use the feeler gauge. The MDF surface is plenty hard enough that you won't need to be concerned about the tip of an end mill throwing off your z measurement.
Randall, please add any additional input you think will help.
-ShopBot Buddy PRSAlpha CNC