So it sounds like you have made the saddle a good fit on the boiler dia, if you now add 0.016" of gasket then the saddle will make good contact at the sides but not in the middle.
Options are to not use a gasket and go with a modern sealer as Fizzy suggests, or increase the radius of the saddle to take into account the gasket thickness which is best done by finding some abrasive sheet that is as close as posible to 0.016" and wrap some round the boiler. Now just rub the saddle over this in teh vacinity of where it will eventually fit until you have sanded the whole underside.
Going upto 5BA won't be a problem but you may need to use 6BA heads as there is very little room particularly front and back. To save snapping weaker bronze or stainless screws use steel ones first of all to pull thing sdown and then test once sealant has set. If all is OK then replace steel screws one at a time ading a bit of sealant to each new screw.