I seriously doubt there's much you can do to change the basic nature of the machine. The large area and the thin base would work together to essentially make a random surface. Fire up the vacuum and the forces imparted to the frame and base are uneven. It is impossible to surface the spoilboard under load conditions since you need it to be open and the vacuum off to surface it. A good test would be to surface the spoilboard, then place a sheet of plastic over it, turn on the vacuum and then check the tolerance of the table. I'd bet you'll be surprised at how much variation you'll find.
Then there's the temperature issue. How much variation is the temperature of the machine from the start of the day to steady production? Unless you have quite good climate control and can keep everything at the same temperature all day, you're going to see significant fluctuations in the tolerances of everything. The spoilboard is probably irrelevant or close to it. Trupan is pretty weak and flexible.
ShopBot Details:
PRS Alpha 96x60x12
4hp Spindle
12" indexer
Aspire
Rhino