Sorry about taking so long to respond. First, if you intend to use the #5 for rough work then it really doesn’t have to be super flat. Second, pits in a plane sole, even on a smooth plane, are not a big issue with one possible exception that I will go into later.
Current wisdom says that the plane sole only needs to be as flat as the work demands so that planes for rough work such as scrub work or fore plane type work can really be just “kinda’ sorta flat” and pits won’t matter much since you normally follow the initial work with other planes anyway. I just hope you haven’t done any significant damage at this point so that lapping won’t be a major chore, Planes ride on the high points of the sole so that the general flatness of that surface is what matters most. The exception to the statement about pits is that they can cause some problems if they are at the front of the plane mouth during smoothing type operations. If the pits are very large and are right at that edge then they can allow for lifting of areas of the shaving, especially in highly figured woods, which can add to some tear-out. Really this is normally a minor issue under most circumstances and I have never had any problems with it in the pitted antiques I own. Save “super-tuning” for the smoothers.
To give you some idea, I acquired a Lie-Nielsen low angle jointer that had a run in with a disk grinder, The grinder gouged one side and the sole. After some limited lapping I found that the plane still performed well because the damage is in areas that really don’t affect the function of the plane in any significant way. Lie-Nielsen could possibly grind it out for me for a nominal sum but it would lighten and weaken the plane so why worry about it.
The only times my planes see files is, when I remove raised burrs from dropped plane soles, I ease plane sole edges, and if I have to work on the mouths of the planes for some reason.