I wouldn’t hold back from submitting spectra. (You could have a look in the databases for other ALPY spectra to see how their calibration looks.) I think a wavelength calibration accuracy of ~1/4 the resolution is still good (At the end of the day my ALPY spectra using just the lamp lines are no more accurate. The errors are just at the other end of the wavelength range). There is still something niggling to do with the difference in how the ALPY sees the lamp compared with the star to nail down here but I suspect it will turn out to be something common to ALPYs in general.
Dont refocus to sharpen up the lines in the far red to the detriment of the blue end. The ALPY performance is biased towards the blue end where it actually outperforms the LISA
I think ISIS is finding the lines OK so exposing more probably will not make much difference but exposing for the brightest line that ISIS uses is a good idea and if you want to try going further you can sum several exposures to increase the signal/noise in the faint lines in the same way as summing flats works (I used to do this but the results using just one well exposed lamp exposure seemed to work just as well.)