Unfortunately this is a common issue with a number of brands beyond Marlin. Two common fixes that rely on the amount of misalignment. Set the reciever in a mill vise and with a carbide end mill cut blind holes to accept helicoil inserts. Retains alignment, looks professional and may not need oversized screws which may then lead to drilling out the rail screw holes. At 20 thou misalignment with a 6x32/6×40s or similar screw size, you may need to go to 3.5 x 0.75 screws, 4 x 0.7 at worst or 8x32s/40s if so inclined. I go metric because of A cheap, B helicoils are easily available. Torx, cap or slot screws are easily found in metric. BA threads, best of luck.
Now if its really badly aligned, forget the above. Tig weld the holes, drill and tap on correct alignment. Or split the center, drill and tap a single hole in the reciever and rail and have three screws holding assuming as you say the two rear holes are correct.
Finally if welding or helicoils are not an option, end mill over size holes on the right alignment, tap to whatever, plug the holes with threaded rod or long screws and a heap of 680 loctite, cut off the excess and dress to reciever profile then drill and tap the plugs to the right size and alignment. Under the rail nobody is the wiser and is strong and secure.
The reason i say use an endmill is because they cut precisely, drills follow a cooked hole and replicate the error.
Personally my preference with what you have described on a Marlin is helicoil the 4 holes to 3.5mm and modify the rail/bases to suit if needed. Properly done looks neat and contrary to uninformed opinion, helicoils are stronger than the original thread.
I do hundreds of thread saving jobs yearly. Cost of doing two recoils on a Remlin as i described above would be around half an hour, cost of two helicoils and a bit of GST. Find a gunsmith who was a machinist or tool maker first and i say this because if done wrong, this can turn into a major cluster.
Believe it or not, your ailment with this Marlin is a really simple fix.