That motor does look as if it's protruding rather a lot.
From one of the pictures it appears that the body is just resting on top of the rear boot outriggers, once they're cut down and sitting about 4" up inside the shell the front edge of the bonnet should rise up a little.
Is it just the front of the engine that's proud of the bonnet opening? If so, dropping the back of the shell over the outriggers may help with the engine clearance, but it may also make your seat a bit too high.
You mention that the supplied floorpans are not fit for purpose, is your seat on a flat floor at the moment? If it is I'd recommend you make up some lowered pans as you don't want your driving position to be too high up or your ears will ruin the aerodynamics...
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