It is a common problem with Quality Control that these holes do not align properly, and have been various sizes over the years with the old style Mamods. I cannot comment on an MSS, but recent experience with an MSS spare part bought from Dream Steam tells me that they have similar Quality Control issues as well. It happened with the cylinder back plates as well, where the hole in the cylinder would not line up with the 2 holes in the back plate, leading to a loco that would never run. The screws are only used to secure the valve body to the chassis frame, but there is enough slack to have one of your steam/exhaust holes partly blocked.Surely the reverser will line up though due to the bolts that go in?
The securing screw cannot leak steam as it screws into the middle of the rotating valve body - the steam/exhaust flow through the cut outs in this rotating valve. A recommended modification is to add a 2nd spring, using a washer to space it from the other spring on this screw, which will increase the force holding the rotating valve to the body & hopefully make a more steam tight seal. It is impossible to completely stop steam leaking from this valve, but by lapping the surfaces & adding a 2nd spring you will reduce it to a minimum.
I got my oil resistant gasket paper off ebay - http://cgi.ebay.co.uk/Flexoid-oil-resis ... dZViewItem
The idea actually came from my IP Jane as it has these gaskets fitted. If you do not want to spend £5, then PM me your address & I send you 2 pieces from my stock (will be a delay in posting as I'm currently working Mon - Fri away from home/internet access).