Bought a wrecked 98 XC600 twin, the air box is missing so I bought two UNI foam filters. Does anyone know a "rule of thumb" for jetting carbs after removing the air box.

I would replace the airbox. The UNI foam filters will become very finicky under different conditions and will require a
huge jump in jet sizes (as many as 4-5 jet sizes). At high speeds you will encounter a rich condition due to the
pressure under the hood (inside air draw) and in powder conditions you'll suffocate the carbs if you pack all your
hood vents with powder. Dyno tests have also proven that a free-flowing (outside draw) airbox produces more power
than the socks and are all around more user friendly than the foam filters.