Hey @Kinch
I am not very good at image processing. The only way I am able to get decent images is to blatantly steal techniques from folks kind enough to share them.
If it's of any use to you...
I use PixInsight for the mosaic creation and I use @harry s wonderful tutorial to do it. You can find that here:
http://harrysastroshed.com/pixinsight/pixinsight%20video%20html/pixinsighthomeinter.html
This method has always worked very well for me (quick tip... if any joining edge in your mosaic has an overscan region (black row or column of pixels) make sure those get cropped out before using this method)
Then... for general processing of narrowband images, I use AstroAnarchy's "Tone Mapping" technique. I think @joelshort might use this too. The latest image I posted here is a mosaic and uses tone mapping. I'm pretty happy with this methodology in general.
An explanation here:
https://astroanarchy.blogspot.com/2009/11/power-of-tone-mapping.html
A PDF with more detailed instructions:
http://dl.dropbox.com/u/24702393/Tone%20Mapping.pdf