So the thing has a centrifugal supercharger feeding the throttle body of the RamJet......

Two things come to mind: first the MAP sensor. If you are running boost, you need a 2bar or 3 bar sensor instead of a normally aspirated 1bar sensor. Can you disconnect the supercharger belt and will it run? If so, does the problem go away?

The RamJet uses either a MEFI3 or a MEFI4 controller (Mercury Marine). You should be able to find out if there are mods required to run a boosted engine.....one source is Arizona Speed and Marine in Chandler, AZ. I am sure that there are a lot of others familiar with the programming of a MEFI