You can safely raise the intake and exhaust port the same amount you drop the cylinder. The amount you drop the cylinder is goverened by the amount of clearance between the cylinderhead and the piston, we refer to this clearance as "squish". Small bores like 40 mm can get by with .015 clearance but this clearance needs to increase with bore diameter, on the 044 at or around 50 mm I like to have .019 clearance. If the base gasket can be eliminated the cylinder can be dropped the thickness of the gasket, say .015 for the sake of arguments, if there is still .019 or more clearance after eliminating the gasket then the engine can be run without the gasket and the intake and exhaust ports can be raised .015, the same amount that the cylinder was dropped.
Pioneerguy600