Change loops to use int instead of long

[biboyd]

Addresses issue #426 . Some loops were using long instead of int when this was not actually desired. Found a couple more cases of this in MaestroMakeGrav.cpp where again the index r was just used to access BaseStateArray's

[zingale]

tests pass: http://groot.astro.sunysb.edu/MAESTROeX/test-suite/gfortran/2024-04-11-002/index.html