Just remember, if you mill the intake surface, the bolt threads will be shorter and you have more of a chance to bottom out and not get the housing tight enough to prevent a leak. Shorter bolts, double flat washers, or double gaskets are your only options. I don't like using taps to clean threads but I do use thread chasers and follow up by blowing out the blind bolt hole with compressed air.
thanks , I did add washers but probably best to double up. The machinist is in the family and he said he didnt take much off, i wish i knew how much. Still got enough thread to add those washers which is helpful.