I know that there are people that reprogram their automobile ROMs. I think that altering timing, pressure, and amount of fuel injection is not going to be a problem.
It's the fuel system plumbing that's going to be a problem for home rebuilders.
Why not just swap out the engine and fuel tank when your old system breaks down at 200K miles? Use a new system from GM or Chrysler or Toyota that is already designed for their model for that year? Just have them make a million cars and two million engines and fuel tanks.

Generally, by the time a vehicle's engine has worn out in normal use, so has much of the rest of the vehicle.  It makes more sense to recycle it and build a whole new one, with all the improvements of the intervening time.