I'm not sure what you mean by this. Are you still getting the same error, related to quilting, when running wrf?It runs only for namelist.input. I can't post the one before running.
I recently faced a similar issue and managed to solve it.Unfortunately since I am unable to repeat the issue, it's difficult for me to provide assistance. At this point, I would recommend downloading (or using "git clone") a new version of WRF and reinstalling it, and then trying again. If you don't necessarily need an older version of WRF (e.g., V4.0), I would recommend getting the latest version (V4.5.2). If you get past the issue, let us know how it was resolved.
module_io_quilt_old.F 2931 F
-------------- FATAL CALLED ---------------
FATAL CALLED FROM FILE: <stdin> LINE: 6528
ERROR reading namelist namelist_quilt
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