So, if I understand your post correctly, the governor protrudes from the governor housing by an amount more than the gasket thickness. If you put the governor in the housing and lay a straight edge across it, you should be able to measure with feeler gauges to get a figure. Perhaps at some point in the past someone sanded down the housing to make up for a (thicker) home made gasket?
The governor's purpose is to lower the oil pressure at idle and low engine speeds. For what its worth, I am not really sure you need it. The '48-'57 service manual contains a service bulletin that outlines disabling the governor on '48 and later models. I have been doing this on Knuckles for 30 years and have never seen any problems associated with it. The only possible down side that I can envision is the possibility of the top end over oiling and not returning quick enough, and that only if the pinion bushing clearance was at the low end of tolerance and the rocker arm to shaft clearances were very loose, allowing the extra pressure to find its way to the heads.
There was a block off plate that took the place of the thin center plate, or you can just plug both feed and return holes in the governor housing (leave the governor valve out) and use your stock plate.
Maybe someone can propose a good reason not to do this.....