1) This will show you the difference between the stock '35-41 three-bolt single-chamber master cylinder on the right and the two-bolt dual-chamber replacement unit provided in the kit. Check your floor-to-master cylinder clearance, although the tin lid can be compressed if necessary or the floor may need to be cleared for the slightly taller master cylinder cover.
2 & 3) The holes on both sides of the adapter plate are countersunk for head clearance when all is bolted together. The two outside holes for the dual-chamber master cylinder are countersunk on the other side. The plate does not go on the old master cylinder, it simply picks up the same hole pattern on the stock Ford pedal bracket.
(4) The side of the adapter (far back) attaches to the stock pedal bracket on the frame. This is why the adapter has countersunk holes on the master cylinder side.