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A3: While many warm pixels are caught by the outlier detection step in the calwebb_spec3 pipeline prior to combination of the data into final dither-combined 3-D data cubes, some bright pixels nonetheless make it through into the cubes. 
There is a now an option for bad pixel self-calibration in spec2.  When you turn on bad pixel self-calibration, all exposures on a given detector are used to find and flag bad pixels that may have been missed by the bad pixel mask. This works best when dedicated background observations are included (if you have an extended source with no dedicated background it will not work).  Please see this workbook: https://github.com/spacetelescope/jwst-pipeline-notebooks/blob/main/notebooks/MIRI/MRS/JWPipeNB-MIRI-MRS.ipynb
Please try out this step and see what your results are.  

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Q4:  My NIRSpec data has an imprint that I'm trying to remove, what is the best way to do this? 

A4:    You can download the association file from mast and then feed it into the pipeline for help tackling the issue. 

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Q5: I have a few questions about noise in MIRI-MRS spectroscopy.  I am working on several projects which are doing deep observations of faint sources and there is noise that seems to have structure in spectral and spatial coordinates even after pixel-based background subtraction.  I am wondering about strategies to reduce this noise.

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